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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 (506) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 17,985 39,352 7
Proteins 11,363 25,841 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) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000000001925 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000000000001314 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00009276 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 0.005241 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 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 0.00000003135 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000002101 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.00007567 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1811 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3378 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.9918 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.009802 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.7128 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.9841 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.4227 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.3125 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.2195 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.007982 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.05214 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.8759 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.001918 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.08763 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.001253 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2551 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.06272 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.323 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.9032 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.3304 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.005122 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.3736 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.0129 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.0291 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.003106 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.02442 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.008905 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.2679 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.000000000000003734 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0000000005071 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000000001025 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.00000001367 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.00000001467 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0000002362 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0000006441 Informative Direct
Biological Process (BP) cellular response to lipid 0.000000785 Informative Direct
Biological Process (BP) regulation of cellular localization 0.000001241 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.000002791 Informative Direct
Biological Process (BP) response to wounding 0.00001123 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.00001704 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.00002837 Informative Direct
Biological Process (BP) regulation of transferase activity 0.00003557 Informative Direct
Biological Process (BP) regulation of cell cycle 0.0000421 Informative Direct
Biological Process (BP) regulation of catabolic process 0.00004878 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.00006015 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0009199 Informative Direct
Biological Process (BP) hemopoiesis 0.0009357 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0009422 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.001457 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.8157 Informative Inherited
Biological Process (BP) response to bacterium 0.153 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.002187 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.3956 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.00122 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.3357 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.2642 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.2467 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.4052 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.4814 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.5895 Informative Inherited
Biological Process (BP) phosphorylation 0.01062 Informative Inherited
Biological Process (BP) regulation of peptide transport 0.02306 Informative Inherited
Biological Process (BP) regulation of protein localization 0.0704 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.001182 Informative Inherited
Biological Process (BP) cell activation 0.01675 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) regulation of RNA stability 0 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 0.00000000000005058 Highly Informative Direct
Biological Process (BP) response to glucocorticoid 0.00000000000006022 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.00000000000008578 Highly Informative Direct
Biological Process (BP) regulation of hemopoiesis 0.000000000000897 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.00000000002309 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.0000000004345 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.000000001468 Highly Informative Direct
Biological Process (BP) positive regulation of cellular catabolic process 0.000000003213 Highly Informative Direct
Biological Process (BP) MAPK cascade 0.00000001359 Highly Informative Direct
Biological Process (BP) response to growth factor 0.000000582 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0.0000006459 Highly Informative Direct
Biological Process (BP) RNA splicing 0.000001919 Highly Informative Direct
Biological Process (BP) negative regulation of homeostatic process 0.000002098 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.0000548 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell proliferation 0.00005954 Highly Informative Direct
Biological Process (BP) regulation of mitotic cell cycle phase transition 0.00007084 Highly Informative Direct
Biological Process (BP) mRNA processing 0.00008353 Highly Informative Direct
Biological Process (BP) regulation of viral process 0.0001096 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.0001132 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0.0001523 Highly Informative Direct
Biological Process (BP) leukocyte differentiation 0.0001976 Highly Informative Direct
Biological Process (BP) lymphocyte activation 0.0002176 Highly Informative Direct
Biological Process (BP) negative regulation of multi-organism process 0.0003358 Highly Informative Direct
Biological Process (BP) cellular response to biotic stimulus 0.0004085 Highly Informative Direct
Biological Process (BP) gene silencing 0.0007955 Highly Informative Direct
Biological Process (BP) negative regulation of mitotic cell cycle 0.001432 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle phase transition 0.008046 Highly Informative Inherited
Biological Process (BP) response to molecule of bacterial origin 0.01157 Highly Informative Inherited
Biological Process (BP) negative regulation of cytokine production 0.08405 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.3152 Highly Informative Inherited
Biological Process (BP) protein modification by small protein conjugation 0.002261 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3371 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000000002668 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 0.0002393 Informative Direct
Molecular Function (MF) enzyme binding 0.05122 Informative Inherited
Molecular Function (MF) ubiquitin-like protein transferase activity 0.00008835 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.4682 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.1264 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.5919 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.07935 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.001689 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.0000000000005364 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00001286 Informative Direct
Cellular Component (CC) chromosome 0.2897 Informative Inherited
Cellular Component (CC) pole plasm 0.00000008932 Highly Informative Direct
Cellular Component (CC) CCR4-NOT complex 0.0000002258 Highly Informative Direct
Cellular Component (CC) protein serine/threonine phosphatase complex 0.0000004769 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.000002167 Highly Informative Direct
Cellular Component (CC) chromatin 0.0001524 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processUbl conjugation pathway0.000000000000005672Moderately InformativeDirect
Biological processHost-virus interaction0.006859Moderately InformativeInherited
Biological processmRNA processing0InformativeDirect
Biological processNeurogenesis0.0003834InformativeDirect
Biological processmRNA transport0.000000000000006138Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Cellular componentHost cytoplasm0.00002638InformativeDirect
Cellular componentExosome0.0000000299Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.0000001395Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00000000000006885Moderately InformativeDirect
Post-translational modificationRepressor0.00000001048Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.0000000001302Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.00007189Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]