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InterPro-Version: 108.0
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{
"metadata": {
"accession": "IPR000690",
"entry_id": null,
"type": "domain",
"go_terms": [
{
"identifier": "GO:0003676",
"name": "nucleic acid binding",
"category": {
"code": "F",
"name": "molecular_function"
}
},
{
"identifier": "GO:0008270",
"name": "zinc ion binding",
"category": {
"code": "F",
"name": "molecular_function"
}
},
{
"identifier": "GO:0005634",
"name": "nucleus",
"category": {
"code": "C",
"name": "cellular_component"
}
}
],
"source_database": "interpro",
"member_databases": {
"profile": {
"PS50171": "Zinc finger matrin-type profile"
}
},
"integrated": null,
"hierarchy": {
"accession": "IPR013087",
"name": "Zinc finger C2H2-type",
"type": "Domain",
"children": [
{
"accession": "IPR003604",
"name": "Matrin/U1-C-like, C2H2-type zinc finger",
"type": "Domain",
"children": [
{
"accession": "IPR000690",
"name": "Matrin/U1-C, C2H2-type zinc finger",
"type": "Domain",
"children": [
{
"accession": "IPR013085",
"name": "U1-C, C2H2-type zinc finger",
"type": "Domain",
"children": []
}
]
}
]
},
{
"accession": "IPR022755",
"name": "Zinc finger, double-stranded RNA binding",
"type": "Domain",
"children": []
},
{
"accession": "IPR031514",
"name": "Aberrant zinc-finger domain",
"type": "Domain",
"children": []
},
{
"accession": "IPR034729",
"name": "Zinc finger CCHC HIVEP-type",
"type": "Domain",
"children": []
},
{
"accession": "IPR034731",
"name": "Zinc finger CCHC FOG-type",
"type": "Domain",
"children": []
},
{
"accession": "IPR041057",
"name": "ZHX, C2H2 finger domain",
"type": "Domain",
"children": []
},
{
"accession": "IPR048403",
"name": "Zinc finger 512, zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR048414",
"name": "Histone-lysine N-methyltransferase PRDM9-like, C2H2 zinc finger-like",
"type": "Domain",
"children": []
},
{
"accession": "IPR048420",
"name": "Zap1-like, C2H2 zinc finger 1",
"type": "Domain",
"children": []
},
{
"accession": "IPR049009",
"name": "Protein arginine N-methyltransferase 3, C2H2 zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR054177",
"name": "Uncharacterized protein B-129, C2H2 zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR055186",
"name": "BIRD-IDD transcription factor, second C2H2 zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR055187",
"name": "BIRD-IDD transcription factor, third C2HC zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR056380",
"name": "ASCIZ, forth C2H2 zinc finger domain",
"type": "Domain",
"children": []
},
{
"accession": "IPR056436",
"name": "ZIC1-5/GLI1-3like, C2H2 zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR056438",
"name": "CTCF-like, C2H2 zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR056545",
"name": "ASCIZ, first and second C2H2 zinc finger domains",
"type": "Domain",
"children": []
},
{
"accession": "IPR057829",
"name": "ZNF142, C2H2 zinc finger 21/23",
"type": "Domain",
"children": []
},
{
"accession": "IPR059009",
"name": "C2H2-domain containing protein, first zinc finger domain",
"type": "Domain",
"children": []
},
{
"accession": "IPR059042",
"name": "ZNF598, C2H2 zinc finger domain",
"type": "Domain",
"children": []
},
{
"accession": "IPR059058",
"name": "Zinc finger protein 462, C2H2 zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR059059",
"name": "Zinc finger protein 462-like, seventh C2H2 zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR059074",
"name": "Z280C/D-like, C2H2 zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR059095",
"name": "C2H2-domain containing protein, second zinc finger domain",
"type": "Domain",
"children": []
},
{
"accession": "IPR060130",
"name": "CASZ1-like, zinc finger",
"type": "Domain",
"children": []
},
{
"accession": "IPR060750",
"name": "Tri6-like, C2H2 zinc finger domain",
"type": "Domain",
"children": []
}
]
},
"name": {
"name": "Matrin/U1-C, C2H2-type zinc finger",
"short": "Matrin/U1-C_Znf_C2H2"
},
"description": [
{
"text": "<p>Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [[cite:PUB00035807], [cite:PUB00035805], [cite:PUB00035806], [cite:PUB00035804], [cite:PUB00014077]]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [[cite:PUB00035812]]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.</p>",
"llm": false,
"checked": false,
"updated": false
},
{
"text": "<p>C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short β-hairpin and an α-helix (β/β/α structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 [[cite:PUB00035808]]. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes [[cite:PUB00035809]]. Transcription factors usually contain several Znf's (each with a conserved β/β/α structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short α-helix in the Znf, the Znf spanning 3-4 bases of the DNA [[cite:PUB00035811]]. C2H2 zinc fingers can also bind to RNA and protein targets [[cite:PUB00043274]].</p>",
"llm": false,
"checked": false,
"updated": false
},
{
"text": "<p>A specific C2H2 Znf is conserved in matrin and several RNA-binding proteins. The Znf follows the general pattern C-x2-C-x(12,16)-H-x5-H, and is different from the 'classical' DNA-binding C2H2 Znf.</p>",
"llm": false,
"checked": false,
"updated": false
}
],
"wikipedia": null,
"literature": {
"PUB00035807": {
"PMID": 10529348,
"ISBN": null,
"volume": "293",
"issue": "2",
"year": 1999,
"title": "Zinc finger peptides for the regulation of gene expression.",
"URL": null,
"raw_pages": "215-8",
"medline_journal": "J Mol Biol",
"ISO_journal": "J. Mol. Biol.",
"authors": [
"Klug A."
],
"DOI_URL": "http://dx.doi.org/10.1006/jmbi.1999.3007"
},
"PUB00035808": {
"PMID": 11361095,
"ISBN": null,
"volume": "58",
"issue": "4",
"year": 2001,
"title": "Three classes of C2H2 zinc finger proteins.",
"URL": null,
"raw_pages": "625-35",
"medline_journal": "Cell Mol Life Sci",
"ISO_journal": "Cell. Mol. Life Sci.",
"authors": [
"Iuchi S."
],
"DOI_URL": "http://dx.doi.org/10.1007/PL00000885"
},
"PUB00035805": {
"PMID": 15963892,
"ISBN": null,
"volume": "15",
"issue": "3",
"year": 2005,
"title": "Multiple modes of RNA recognition by zinc finger proteins.",
"URL": null,
"raw_pages": "367-73",
"medline_journal": "Curr Opin Struct Biol",
"ISO_journal": "Curr. Opin. Struct. Biol.",
"authors": [
"Hall TM."
],
"DOI_URL": "http://dx.doi.org/10.1016/j.sbi.2005.04.004"
},
"PUB00035806": {
"PMID": 15718139,
"ISBN": null,
"volume": "15",
"issue": "1",
"year": 2005,
"title": "Zinc finger proteins: getting a grip on RNA.",
"URL": null,
"raw_pages": "94-8",
"medline_journal": "Curr Opin Struct Biol",
"ISO_journal": "Curr. Opin. Struct. Biol.",
"authors": [
"Brown RS."
],
"DOI_URL": "http://dx.doi.org/10.1016/j.sbi.2005.01.006"
},
"PUB00035809": {
"PMID": 10664601,
"ISBN": null,
"volume": "8",
"issue": "2",
"year": 2000,
"title": "The origin of prokaryotic C2H2 zinc finger regulators.",
"URL": null,
"raw_pages": "77-81",
"medline_journal": "Trends Microbiol",
"ISO_journal": "Trends Microbiol.",
"authors": [
"Bouhouche N",
"Syvanen M",
"Kado CI."
],
"DOI_URL": "http://dx.doi.org/10.1016/S0966-842X(99)01679-0"
},
"PUB00043274": {
"PMID": 18253864,
"ISBN": null,
"volume": "50",
"issue": "3",
"year": 2008,
"title": "Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.",
"URL": null,
"raw_pages": "111-31",
"medline_journal": "Cell Biochem Biophys",
"ISO_journal": "Cell Biochem. Biophys.",
"authors": [
"Brayer KJ",
"Segal DJ."
],
"DOI_URL": "http://dx.doi.org/10.1007/s12013-008-9008-5"
},
"PUB00035804": {
"PMID": 17210253,
"ISBN": null,
"volume": "32",
"issue": "2",
"year": 2007,
"title": "Sticky fingers: zinc-fingers as protein-recognition motifs.",
"URL": null,
"raw_pages": "63-70",
"medline_journal": "Trends Biochem Sci",
"ISO_journal": "Trends Biochem. Sci.",
"authors": [
"Gamsjaeger R",
"Liew CK",
"Loughlin FE",
"Crossley M",
"Mackay JP."
],
"DOI_URL": "http://dx.doi.org/10.1016/j.tibs.2006.12.007"
},
"PUB00035811": {
"PMID": 10940247,
"ISBN": null,
"volume": "29",
"issue": null,
"year": 2000,
"title": "DNA recognition by Cys2His2 zinc finger proteins.",
"URL": null,
"raw_pages": "183-212",
"medline_journal": "Annu Rev Biophys Biomol Struct",
"ISO_journal": null,
"authors": [
"Wolfe SA",
"Nekludova L",
"Pabo CO."
],
"DOI_URL": "http://dx.doi.org/10.1146/annurev.biophys.29.1.183"
},
"PUB00035812": {
"PMID": 11179890,
"ISBN": null,
"volume": "11",
"issue": "1",
"year": 2001,
"title": "Zinc finger proteins: new insights into structural and functional diversity.",
"URL": null,
"raw_pages": "39-46",
"medline_journal": "Curr Opin Struct Biol",
"ISO_journal": "Curr. Opin. Struct. Biol.",
"authors": [
"Laity JH",
"Lee BM",
"Wright PE."
],
"DOI_URL": "http://dx.doi.org/10.1016/S0959-440X(00)00167-6"
},
"PUB00014077": {
"PMID": 12665246,
"ISBN": null,
"volume": "54",
"issue": "6",
"year": 2002,
"title": "Zinc fingers--folds for many occasions.",
"URL": null,
"raw_pages": "351-5",
"medline_journal": "IUBMB Life",
"ISO_journal": "IUBMB Life",
"authors": [
"Matthews JM",
"Sunde M."
],
"DOI_URL": "http://dx.doi.org/10.1080/15216540216035"
}
},
"set_info": null,
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"counters": {
"subfamilies": 0,
"domain_architectures": 0,
"interactions": 0,
"matches": 21280,
"pathways": 6,
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"proteomes": 3368,
"sets": 0,
"structural_models": {
"alphafold": 18058,
"bfvd": 0
},
"structures": 60,
"taxa": 9607
},
"entry_annotations": {},
"cross_references": {
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"displayName": "PROSITE Doc",
"description": "PROSITE is a database of protein families and domains.",
"rank": 18,
"accessions": [
{
"accession": "PDOC50171",
"url": "http://prosite.expasy.org/PDOC50171"
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}
},
"is_llm": false,
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"is_updated_llm": false,
"representative_structure": null
}
}
