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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 (500) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 17,794 16,537 7
Proteins 11,215 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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000000000000001912 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000000003705 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000000000001136 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00009163 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) biological regulation 0.002397 Least Informative Inherited
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000003297 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0001135 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.0001185 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.07742 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1541 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.3311 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.361 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.009965 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.01116 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.6743 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) cell communication 0.9848 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.9907 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.002321 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.007885 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.3419 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2358 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.2373 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.02579 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.005117 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.4539 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.3165 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.009624 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.8806 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.3614 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.001035 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.00386 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.02762 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.9979 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.07244 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.244 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.8476 Moderately Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.0000000000168 Informative Direct
Biological Process (BP) response to cytokine 0.0000000002929 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0000000004559 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0000000008645 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.00000002197 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.00000002359 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0000002001 Informative Direct
Biological Process (BP) cellular response to lipid 0.0000003009 Informative Direct
Biological Process (BP) regulation of cellular localization 0.0000008452 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.000001158 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.000001482 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.00001758 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.00003359 Informative Direct
Biological Process (BP) regulation of transferase activity 0.00003631 Informative Direct
Biological Process (BP) regulation of catabolic process 0.00004242 Informative Direct
Biological Process (BP) regulation of cell cycle 0.00004855 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.0001174 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0005432 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0006531 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.0008153 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.0009693 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.001004 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.8053 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.6209 Informative Inherited
Biological Process (BP) response to bacterium 0.1304 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.003139 Informative Inherited
Biological Process (BP) cell activation 0.01684 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.3425 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.2407 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.4496 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.3106 Informative Inherited
Biological Process (BP) phosphorylation 0.01019 Informative Inherited
Biological Process (BP) regulation of peptide transport 0.02253 Informative Inherited
Biological Process (BP) regulation of protein localization 0.07162 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) positive regulation of transport 0.8251 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.01287 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.3802 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.5012 Informative Inherited
Biological Process (BP) regulation of RNA stability 0 Highly Informative Direct
Biological Process (BP) response to glucocorticoid 0.00000000000002092 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 0.00000000000003418 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.000000000001458 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.00000000002624 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.0000000003868 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.000000001243 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.00000001077 Highly Informative Direct
Biological Process (BP) MAPK cascade 0.00000002165 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.0000002419 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0.0000007821 Highly Informative Direct
Biological Process (BP) RNA splicing 0.000001463 Highly Informative Direct
Biological Process (BP) negative regulation of homeostatic process 0.000002225 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.000003137 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell proliferation 0.00005674 Highly Informative Direct
Biological Process (BP) mRNA processing 0.00007329 Highly Informative Direct
Biological Process (BP) regulation of viral life cycle 0.00007728 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.0001161 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0.0001857 Highly Informative Direct
Biological Process (BP) lymphocyte activation 0.0002281 Highly Informative Direct
Biological Process (BP) leukocyte differentiation 0.0002496 Highly Informative Direct
Biological Process (BP) cellular response to biotic stimulus 0.0003677 Highly Informative Direct
Biological Process (BP) gene silencing 0.0007853 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.0009839 Highly Informative Direct
Biological Process (BP) negative regulation of mitotic cell cycle 0.001339 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle phase transition 0.009023 Highly Informative Inherited
Biological Process (BP) response to molecule of bacterial origin 0.008997 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.35 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.3386 Highly Informative Inherited
Biological Process (BP) negative regulation of multi-organism process 0.001051 Highly Informative Inherited
Biological Process (BP) cell division 0.02595 Highly Informative Inherited
Biological Process (BP) protein modification by small protein conjugation 0.002174 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000000008067 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) transporter activity 1 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.0001784 Informative Direct
Molecular Function (MF) enzyme binding 0.02765 Informative Inherited
Molecular Function (MF) ubiquitin-like protein transferase activity 0.00008677 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0.00000000000008854 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.4863 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.1078 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.5842 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.091 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.002271 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.0000000000007368 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00003537 Informative Direct
Cellular Component (CC) chromosome 0.1177 Informative Inherited
Cellular Component (CC) pole plasm 0.0000001037 Highly Informative Direct
Cellular Component (CC) CCR4-NOT complex 0.0000002147 Highly Informative Direct
Cellular Component (CC) protein serine/threonine phosphatase complex 0.0000004469 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.000001702 Highly Informative Direct
Cellular Component (CC) chromatin 0.0001379 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 phenotype0.2295Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.2409Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.7845Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.1054Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.1086Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal protein level0.1492Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.1608Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.2548Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.0001971InformativeDirect
Mammalian Phenotype (MP)increased gland tumor incidence0.005683InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.006007InformativeInherited
Mammalian Phenotype (MP)abnormal circulating cytokine level0.008689InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.009843InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.009852InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.01487InformativeInherited
Mammalian Phenotype (MP)enlarged lymph nodes0.000008233Highly InformativeDirect
Mammalian Phenotype (MP)increased T cell derived lymphoma incidence0.0002283Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus development0.000275Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.0005996Highly 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 variant0.0006015Least InformativeDirect
Worm Phenotype (WP)cell development variant0.003245Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.01944Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.1394Least InformativeInherited
Worm Phenotype (WP)retarded heterochronic variations0.8262Least InformativeInherited
Worm Phenotype (WP)cell division variant0.001277Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.1182Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.3662Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant1Moderately InformativeInherited
Worm Phenotype (WP)cell number increased0.00000001431InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.005147InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.01055InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.02323InformativeInherited
Worm Phenotype (WP)RNA expression variant0.06423InformativeInherited
Worm Phenotype (WP)P granule defective0.000000001787Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.000000008487Highly InformativeDirect
Worm Phenotype (WP)slow embryonic development0.0001181Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.01124Highly InformativeInherited
Worm Phenotype (WP)pharyngeal development variant0.01169Highly InformativeInherited
Worm Phenotype (WP)epithelial development variant0.01808Highly InformativeInherited
Worm Phenotype (WP)mRNA expression variant0.1083Highly InformativeInherited
Worm Phenotype (WP)cell number decreased0.3325Highly 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)cell0.002948Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.003452Least InformativeInherited
Xenopus ANatomical entity (XAN)oocyte0.0002858Highly InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0005215Highly 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)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.108Moderately InformativeInherited
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0InformativeDirect
Enzyme Commission (EC)RNA helicase0.0001849InformativeDirect

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 pathway0.000000000000005673Moderately InformativeDirect
Biological processHost-virus interaction0.007932Moderately InformativeInherited
Biological processmRNA processing0InformativeDirect
Biological processNeurogenesis0.0003671InformativeDirect
Biological processmRNA transport0.000000000000005206Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Cellular componentHost cytoplasm0.00002363InformativeDirect
Cellular componentExosome0.00000003045Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.0000001536Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00000000000006954Moderately InformativeDirect
Post-translational modificationRepressor0.00000001041Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.00000134Moderately 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 ]