9CG4 | pdb_00009cg4

Cryo-EM structure of FAN1, PCNA and DNA substrate with (CAG)2 extrusion in intermediate state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth D]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth E]	PF21169	Fanconi-associated nuclease 1, SAP subdomain (Fan1_SAP)	Fanconi-associated nuclease 1, SAP subdomain	This domain is found in Fanconi-associated nuclease 1 from humans (Fan1) and similar proteins from chordates. Fan1 is involved in the processing of DNA interstrand crosslinks (ICLs) and therefore in the maintenance of genomic stability and prevention ...	This domain is found in Fanconi-associated nuclease 1 from humans (Fan1) and similar proteins from chordates. Fan1 is involved in the processing of DNA interstrand crosslinks (ICLs) and therefore in the maintenance of genomic stability and prevention of tissue decline in multiple organs. FAN1 consists of an SAP-containing N-terminal domain, a middle tetratricopeptide repeat domain (TPR) and a C-terminal viral replication and repair nuclease domain (VRR_nuc domain, Pfam:PF08774). This entry represents the SAP subdomain, part of the N-terminal domain. It consists of four alpha-helices [1-3].	Domain
D [auth E]	PF21315	FAN1, HTH domain (FAN1_HTH)	FAN1, HTH domain	FAN1 is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). It maintains genomic stability and prevents tissue decline in several organs. This protein possesses preferential endonuclease activity toward ...	FAN1 is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). It maintains genomic stability and prevents tissue decline in several organs. This protein possesses preferential endonuclease activity toward 5' flap structures [1-5]. FAN1 is present in most eukaryotes and some bacterial sequences. It consists of four characterised domains: UBZ, SAP, TPR and VRR nuclease (Pfam:PF08774). However, monocellular eukaryote and bacterial homologues lack the UBZ domain [1]. The N-terminal helical domain of FAN1 can be subdivided in a winged-helix (WH) DNA-binding domain, represented in this entry, and a SAP domain (bacterial Pfam:PF18081 and eukaryotic Pfam:PF21169) [1-5].	Domain
A [auth B], B [auth C], C [auth D]	PF02747	Proliferating cell nuclear antigen, C-terminal domain (PCNA_C)	Proliferating cell nuclear antigen, C-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
A [auth B], B [auth C], C [auth D]	PF00705	Proliferating cell nuclear antigen, N-terminal domain (PCNA_N)	Proliferating cell nuclear antigen, N-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F	DNA (5'-D(PAPTPCPTPCPGPAPGPTPCPTPAPGPAPAPAPTPTPCPG)-3')	-	-	-
E [auth A]	DNA (5'-D(PCPGPAPAPTPTPTPCPTPAPGPAPCPTPCPGPAPGPAPTPCPAP*G)-3')	-	-	-
D [auth E]	Fanconi-associated nuclease 1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding flap-structured DNA binding nucleic acid binding ubiquitin-modified protein reader activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity 5'-flap endonuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding flap-structured DNA binding nucleic acid binding ubiquitin-modified protein reader activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity 5'-3' exonuclease activity exonuclease activity transition metal ion binding zinc ion binding phosphoric ester hydrolase activity phosphodiesterase I activity phosphoric diester hydrolase activity	cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair nucleotide-excision repair interstrand cross-link repair	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intercellular bridge intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intercellular bridge intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen
A [auth B], B [auth C], C [auth D]	Proliferating cell nuclear antigen	protein-containing complex binding binding hydrolase activity, acting on glycosyl bonds catalytic activity, acting on DNA purine-specific mismatch base pair DNA N-glycosylase activity catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity mismatch base pair DNA N-glycosylase activity protein tyrosine kinase binding protein binding kinase binding protein-containing complex binding binding hydrolase activity, acting on glycosyl bonds catalytic activity, acting on DNA purine-specific mismatch base pair DNA N-glycosylase activity catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity mismatch base pair DNA N-glycosylase activity protein tyrosine kinase binding protein binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding identical protein binding chromatin binding DNA binding DNA insertion or deletion binding double-stranded DNA binding mismatched DNA binding dinucleotide insertion or deletion binding nucleic acid binding mismatch repair complex binding MutLalpha complex binding damaged DNA binding histone acetyltransferase binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear estrogen receptor binding DNA polymerase binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process macromolecule metabolic process replication fork processing leading strand elongation DNA strand elongation DNA strand elongation involved in DNA replication ovulation cycle rhythmic process estrous cycle reproductive process multicellular organismal reproductive process cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication epithelium development cellular developmental process cell differentiation tissue development epithelial cell differentiation translesion synthesis nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process regulation of cellular response to stress positive regulation of response to stimulus positive regulation of DNA repair regulation of response to stress regulation of DNA repair regulation of response to stimulus response to ketone response to lipid response to endogenous stimulus response to glucocorticoid response to oxygen-containing compound response to corticosteroid response to hormone response to steroid hormone response to chemical response to dexamethasone response to acid chemical response to nitrogen compound response to L-glutamate response to amino acid cellular response to chemical stimulus cellular response to xenobiotic stimulus response to xenobiotic stimulus nuclear DNA replication telomere organization cell cycle DNA replication mitotic cell cycle telomere maintenance via semi-conservative replication cellular component organization mitotic telomere maintenance via semi-conservative replication cell cycle cellular component organization or biogenesis cell cycle process chromosome organization telomere maintenance organelle organization mitotic cell cycle process negative regulation of biological process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process gene expression regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process chromatin organization regulation of catalytic activity positive regulation of molecular function positive regulation of deoxyribonuclease activity positive regulation of catalytic activity regulation of molecular function regulation of transferase activity regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA-directed DNA polymerase activity gland development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration cellular response to oxidative stress cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV base-excision repair, gap-filling base-excision repair response to metal ion response to cadmium ion response to estradiol	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure membraneless organelle intracellular membraneless organelle chromatin chromosome PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex male germ cell nucleus germ cell nucleus membrane-enclosed lumen nuclear replication fork nuclear chromosome intracellular organelle lumen organelle lumen replication fork nuclear lumen chromosome, telomeric region chromosomal region PCNA-p21 complex centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton nucleoplasm endomembrane system organelle envelope nuclear envelope nuclear periphery nuclear lamina nuclear body protein-DNA complex replisome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E]	IPR049125	Fanconi-associated nuclease 1-like, winged-helix domain	Domain
D [auth E]	IPR033315	Fanconi-associated nuclease 1-like	Family
D [auth E]	IPR014883	VRR-NUC domain	Domain
D [auth E]	IPR049132	Fanconi-associated nuclease 1-like, eukaryotes	Family
D [auth E]	IPR049126	Fanconi-associated nuclease 1-like, TPR domain	Domain
D [auth E]	IPR049138	Fanconi-associated nuclease 1, SAP subdomain, metazoa	Domain
D [auth E]	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
D [auth E]	IPR006642	Rad18, zinc finger UBZ4-type	Domain
A [auth B], B [auth C], C [auth D]	IPR046938	DNA clamp superfamily	Homologous Superfamily
A [auth B], B [auth C], C [auth D]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
A [auth B], B [auth C], C [auth D]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
A [auth B], B [auth C], C [auth D]	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
A [auth B], B [auth C], C [auth D]	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth E]	Pharos: Q9Y2M0	karyomegalic interstitial nephritis Megalocytic interstitial nephritis chromosome 15q13.3 microdeletion syndrome osteosarcoma Lynch syndrome ovarian cancer
A [auth B], B [auth C], C [auth D]	Pharos: P12004	psoriasis ataxia-telangiectasia-like disorder 2 hepatoblastoma adenocarcinoma malignant colon neoplasm granular cell carcinoma Radiation Injuries, Experimental tubular adenocarcinoma focal segmental glomerulosclerosis pancreatic intraductal papillary-mucinous neoplasm endometriosis primitive neuroectodermal tumor glioblastoma pustulosis palmaris et plantaris Sjogren syndrome psoriasis ataxia-telangiectasia-like disorder 2 hepatoblastoma adenocarcinoma malignant colon neoplasm granular cell carcinoma Radiation Injuries, Experimental tubular adenocarcinoma focal segmental glomerulosclerosis pancreatic intraductal papillary-mucinous neoplasm endometriosis primitive neuroectodermal tumor glioblastoma pustulosis palmaris et plantaris Sjogren syndrome large cell medulloblastoma lung cancer astrocytic tumor nasopharyngeal carcinoma neurodegenerative disease colonic neoplasm ovarian cancer dermatomyositis pituitary cancer IgA glomerulonephritis ischemic disease lung adenocarcinoma ataxia-telangiectasia-like disorder malignant glioma atypical teratoid rhabdoid tumor medulloblastoma brain cancer breast cancer non-small cell lung carcinoma cribriform carcinoma pancreatic intraductal papillary-mucinous carcinoma ductal breast carcinoma in situ invasive ductal breast carcinoma juvenile dermatomyositis lung benign neoplasm lymphoplasmacytic lymphoma ataxia-telangiectasia-like disorder 1 benign colon neoplasm myopathy breast carcinoma oligodendroglioma cribriform carcinoma of breast

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.