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CCCH zinc finger superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   CCCH zinc finger [ 90228]
Superfamily:   CCCH zinc finger [ 90229]
Families:   CCCH zinc finger [ 90230] (4)


Superfamily statistics
Genomes (499) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 17,742 16,537 7
Proteins 11,177 11,033 4


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000000003692 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000000000002845 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00006635 Least Informative Direct
Biological Process (BP) biological regulation 0.01679 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.00000000003031 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00000005541 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000006816 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.0000001411 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0003027 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.1527 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.3146 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.2596 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.00211 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.1305 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.002428 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.003694 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.07344 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1531 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.3109 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.004267 Moderately Informative Inherited
Biological Process (BP) signaling 0.7399 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.9645 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.5379 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.1866 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.03202 Moderately Informative Inherited
Biological Process (BP) cell communication 0.8707 Moderately Informative Inherited
Biological Process (BP) response to stress 1 Moderately Informative Inherited
Biological Process (BP) system development 0.9602 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.002892 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.01554 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.03579 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.2368 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.04137 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.08829 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.04959 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.0000000000001283 Informative Direct
Biological Process (BP) response to cytokine 0.0000000001154 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0000000006543 Informative Direct
Biological Process (BP) regulation of catabolic process 0.00000001828 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00000003413 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0000000712 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0000002009 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.000000297 Informative Direct
Biological Process (BP) regulation of cellular localization 0.0000004212 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.0000006067 Informative Direct
Biological Process (BP) cellular response to lipid 0.0000006127 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.000004009 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.00001107 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.00003871 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.00004255 Informative Direct
Biological Process (BP) regulation of cell cycle 0.00006929 Informative Direct
Biological Process (BP) regulation of transferase activity 0.0001842 Informative Direct
Biological Process (BP) nitrogen compound transport 0.0002484 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0003557 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0003896 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.0007185 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.001851 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.8225 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.002341 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.1919 Informative Inherited
Biological Process (BP) positive regulation of transport 0.7878 Informative Inherited
Biological Process (BP) regulation of protein localization 0.3008 Informative Inherited
Biological Process (BP) cell adhesion 0.05152 Informative Inherited
Biological Process (BP) response to bacterium 0.1012 Informative Inherited
Biological Process (BP) phosphorylation 0.008792 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.3358 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.3484 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.5928 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.2424 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.02125 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.8856 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.004716 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3592 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.4322 Informative Inherited
Biological Process (BP) mRNA metabolic process 0 Highly Informative Direct
Biological Process (BP) cellular response to corticosteroid stimulus 0 Highly Informative Direct
Biological Process (BP) regulation of RNA stability 0 Highly Informative Direct
Biological Process (BP) response to glucocorticoid 0.00000000000001582 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.0000000000001067 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.000000000005279 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.00000000003711 Highly Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.00000000005722 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.0000000001025 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.0000000002752 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.00000000443 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0.00000001871 Highly Informative Direct
Biological Process (BP) MAPK cascade 0.00000002632 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.00000005238 Highly Informative Direct
Biological Process (BP) negative regulation of homeostatic process 0.0000003183 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0000004325 Highly Informative Direct
Biological Process (BP) negative regulation of mitotic cell cycle 0.000001868 Highly Informative Direct
Biological Process (BP) regulation of mitotic cell cycle phase transition 0.000003336 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.00001247 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.0000144 Highly Informative Direct
Biological Process (BP) leukocyte cell-cell adhesion 0.00002533 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell proliferation 0.00004937 Highly Informative Direct
Biological Process (BP) regulation of viral life cycle 0.00005933 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0.0001082 Highly Informative Direct
Biological Process (BP) lymphocyte activation 0.0001681 Highly Informative Direct
Biological Process (BP) cellular response to biotic stimulus 0.0002794 Highly Informative Direct
Biological Process (BP) hemopoiesis 0.0003696 Highly Informative Direct
Biological Process (BP) gene silencing 0.000549 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.0008788 Highly Informative Direct
Biological Process (BP) negative regulation of multi-organism process 0.006961 Highly Informative Inherited
Biological Process (BP) positive regulation of cellular protein localization 0.01555 Highly Informative Inherited
Biological Process (BP) response to molecule of bacterial origin 0.00718 Highly Informative Inherited
Biological Process (BP) cell division 0.006747 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.2235 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0.7174 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.2816 Highly Informative Inherited
Biological Process (BP) protein modification by small protein conjugation 0.001853 Highly Informative Inherited
Molecular Function (MF) binding 0.000000001045 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.9983 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.00004627 Informative Direct
Molecular Function (MF) enzyme binding 0.01828 Informative Inherited
Molecular Function (MF) ubiquitin-like protein transferase activity 0.00006 Highly Informative Direct
Molecular Function (MF) mRNA binding 0.07951 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.1342 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.3531 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.426 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0004591 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.02379 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.0000000000001732 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0000543 Informative Direct
Cellular Component (CC) pole plasm 0.00000009276 Highly Informative Direct
Cellular Component (CC) protein serine/threonine phosphatase complex 0.0000004789 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.000003184 Highly Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.3053Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.3318Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.6827Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.0185Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.09137Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal protein level0.1079Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.1354Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.2038Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.0001097InformativeDirect
Mammalian Phenotype (MP)increased gland tumor incidence0.004332InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.004359InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.004754InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.005962InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.006261InformativeInherited
Mammalian Phenotype (MP)abnormal circulating cytokine level0.006789InformativeInherited
Mammalian Phenotype (MP)enlarged lymph nodes0.000004469Highly InformativeDirect
Mammalian Phenotype (MP)increased T cell derived lymphoma incidence0.0001732Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus development0.0002817Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.0003544Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.0002836Least InformativeDirect
Worm Phenotype (WP)cell development variant0.001295Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.0244Least InformativeInherited
Worm Phenotype (WP)retarded heterochronic variations0.7946Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.02646Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.1191Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.5033Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant1Moderately InformativeInherited
Worm Phenotype (WP)cell number increased0.00000002136InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.00502InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.01069InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.02273InformativeInherited
Worm Phenotype (WP)RNA expression variant0.07092InformativeInherited
Worm Phenotype (WP)P granule defective0.000000001861Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00000002646Highly InformativeDirect
Worm Phenotype (WP)division axis defective0.000000299Highly InformativeDirect
Worm Phenotype (WP)slow embryonic development0.0001488Highly InformativeDirect
Worm Phenotype (WP)pharyngeal development variant0.01164Highly InformativeInherited
Worm Phenotype (WP)lineage variant0.01329Highly InformativeInherited
Worm Phenotype (WP)epithelial development variant0.01441Highly InformativeInherited
Worm Phenotype (WP)mRNA expression variant0.09744Highly InformativeInherited
Worm Phenotype (WP)cell number decreased0.315Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)head0Moderately InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.002883Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.003163Least InformativeInherited
Xenopus ANatomical entity (XAN)oocyte0.0002909Highly InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0003909Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.03063Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0.0002359Moderately InformativeDirect
Enzyme Commission (EC)RNA helicase0.0000001622InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processUbl conjugation pathway0.000000000000004026Moderately InformativeDirect
Biological processHost-virus interaction0.007038Moderately InformativeInherited
Biological processmRNA processing0InformativeDirect
Biological processNeurogenesis0.0003367InformativeDirect
Biological processmRNA transport0.00000000000000379Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Cellular componentHost cytoplasm0.00001427InformativeDirect
Cellular componentExosome0.0000000289Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.0000002326Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding6.999e-16Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00000000000004387Moderately InformativeDirect
Post-translational modificationRepressor0.0000002053Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.000000766Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 6 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a CCCH zinc finger domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 6 hidden Markov models representing the CCCH zinc finger superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]