2A1J

Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2a1ja1	All alpha proteins	SAM domain-like	RuvA domain 2-like	Hef domain-like	DNA repair endonuclease XPF	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2a1jb1	All alpha proteins	SAM domain-like	RuvA domain 2-like	Hef domain-like	DNA excision repair protein ERCC-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2a1jb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Hef domain-like	8024066	4001374	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8036445	3000163	SCOP2 (2022-06-29)
B	SCOP2 Family	Hef domain-like	8024067	4001374	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Helix-hairpin-helix tandem	8036446	3000163	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	HHH_2_1	e2a1jA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2_1	ECOD (1.6)
B	HHH_2_1	e2a1jB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00633	Helix-hairpin-helix motif (HHH)	Helix-hairpin-helix motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA repair endonuclease XPF	TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity DNA binding organic cyclic compound binding damaged DNA binding nucleic acid binding chromatin binding promoter-specific chromatin binding single-stranded DNA endodeoxyribonuclease activity identical protein binding single-stranded DNA binding	sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization organic substance metabolic process heterocycle metabolic process meiosis I nitrogen compound metabolic process meiotic nuclear division cell cycle cellular component organization or biogenesis sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization organic substance metabolic process heterocycle metabolic process meiosis I nitrogen compound metabolic process meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle DNA recombination cellular metabolic process organelle fission cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination organic cyclic compound metabolic process nuclear division organelle organization meiosis I cell cycle process cellular process metabolic process macromolecule metabolic process cellular aromatic compound metabolic process cellular response to stimulus telomere maintenance in response to DNA damage negative regulation of telomere maintenance regulation of cellular process response to stimulus regulation of cellular response to stress negative regulation of biological process telomere organization negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process negative regulation of chromosome organization negative regulation of nucleobase-containing compound metabolic process negative regulation of telomere maintenance in response to DNA damage regulation of nucleobase-containing compound metabolic process regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process regulation of cellular metabolic process regulation of chromosome organization regulation of organelle organization telomere maintenance telomere capping regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process regulation of telomere maintenance regulation of cellular component organization regulation of protection from non-homologous end joining at telomere cellular response to stress response to stress regulation of response to stress negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of telomere maintenance in response to DNA damage negative regulation of response to stimulus protection from non-homologous end joining at telomere biological regulation chromosome organization regulation of macromolecule metabolic process negative regulation of protection from non-homologous end joining at telomere negative regulation of organelle organization DNA damage response negative regulation of telomere capping negative regulation of DNA metabolic process regulation of telomere capping regulation of DNA binding regulation of binding negative regulation of binding negative regulation of molecular function negative regulation of telomeric DNA binding regulation of telomeric DNA binding regulation of double-stranded telomeric DNA binding negative regulation of DNA binding regulation of molecular function negative regulation of double-stranded telomeric DNA binding response to light stimulus response to radiation response to abiotic stimulus response to UV UV protection telomeric DNA-containing double minutes formation telomere maintenance via recombination mitotic recombination nucleotide-excision repair DNA repair nucleotide-excision repair involved in interstrand cross-link repair interstrand cross-link repair recombinational repair double-strand break repair via homologous recombination double-strand break repair cellular response to radiation cellular response to environmental stimulus cellular response to light stimulus cellular response to abiotic stimulus cellular response to UV telomere maintenance via telomere lengthening regulation of telomere maintenance via telomere lengthening negative regulation of telomere maintenance via telomere lengthening catabolic process autophagy regulation of catabolic process regulation of autophagy cellular catabolic process regulation of cellular catabolic process process utilizing autophagic mechanism double-strand break repair via nonhomologous end joining	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle nucleotide-excision repair complex ERCC4-ERCC1 complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle nucleotide-excision repair complex ERCC4-ERCC1 complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nucleotide-excision repair factor 1 complex intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region chromosomal region non-membrane-bounded organelle
B	DNA excision repair protein ERCC-1	TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding DNA binding organic cyclic compound binding damaged DNA binding nucleic acid binding chromatin binding TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding DNA binding organic cyclic compound binding damaged DNA binding nucleic acid binding chromatin binding promoter-specific chromatin binding single-stranded DNA binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development spermatogenesis sexual reproduction multicellular organismal reproductive process male gamete generation gamete generation cellular developmental process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation cell differentiation germ cell development cellular process response to X-ray response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus cell population proliferation cellular response to stimulus telomere maintenance in response to DNA damage negative regulation of telomere maintenance regulation of cellular process regulation of cellular response to stress negative regulation of biological process telomere organization negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process negative regulation of chromosome organization heterocycle metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of telomere maintenance in response to DNA damage regulation of nucleobase-containing compound metabolic process regulation of biological process negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process DNA metabolic process regulation of chromosome organization regulation of organelle organization telomere maintenance organic cyclic compound metabolic process telomere capping regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of telomere maintenance regulation of cellular component organization regulation of protection from non-homologous end joining at telomere cellular component organization organic substance metabolic process cellular response to stress response to stress regulation of response to stress negative regulation of cellular process nitrogen compound metabolic process cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of telomere maintenance in response to DNA damage negative regulation of response to stimulus protection from non-homologous end joining at telomere biological regulation chromosome organization regulation of macromolecule metabolic process negative regulation of protection from non-homologous end joining at telomere nucleic acid metabolic process organelle organization negative regulation of organelle organization DNA damage response negative regulation of telomere capping negative regulation of DNA metabolic process regulation of telomere capping cellular aromatic compound metabolic process replicative senescence interstrand cross-link repair DNA repair cell surface receptor signaling pathway signaling insulin-like growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway response to organic substance response to carbohydrate response to sucrose response to disaccharide response to chemical response to oxygen-containing compound cellular component biogenesis cellular component assembly formation of extrachromosomal circular DNA telomere maintenance via telomere trimming t-circle formation response to light stimulus response to UV UV protection telomeric DNA-containing double minutes formation telomere maintenance via recombination DNA recombination mitotic recombination embryonic organ development embryo development positive regulation of organelle organization positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of telomere maintenance positive regulation of nucleobase-containing compound metabolic process positive regulation of chromosome organization positive regulation of DNA metabolic process positive regulation of t-circle formation positive regulation of cellular component organization regulation of t-circle formation positive regulation of biological process positive regulation of cellular metabolic process positive regulation of cellular process positive regulation of cellular component biogenesis regulation of cellular component biogenesis positive regulation of nitrogen compound metabolic process positive regulation of macromolecule biosynthetic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription cellular biosynthetic process positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of transcription initiation by RNA polymerase II nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II positive regulation of cellular biosynthetic process determination of adult lifespan hemopoiesis post-embryonic development post-embryonic hemopoiesis response to immobilization stress anatomical structure morphogenesis anatomical structure formation involved in morphogenesis syncytium formation nucleotide-excision repair cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation UV-damage excision repair cellular response to abiotic stimulus cellular response to UV adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell activation involved in immune response cell activation involved in immune response leukocyte mediated immunity somatic diversification of immune receptors somatic recombination of immunoglobulin genes involved in immune response immune response immune effector process somatic diversification of immunoglobulins B cell mediated immunity isotype switching immune system development immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination lymphocyte activation leukocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response lymphocyte activation involved in immune response production of molecular mediator of immune response B cell activation cell activation immunoglobulin mediated immune response adaptive immune response immune system process somatic diversification of immune receptors via germline recombination within a single locus response to metal ion response to cadmium ion response to inorganic substance response to extracellular stimulus response to nutrient levels response to nutrient response to external stimulus response to oxidative stress multicellular organism growth developmental growth growth pyrimidine dimer repair by nucleotide-excision repair pyrimidine dimer repair double-strand break repair double-strand break repair via nonhomologous end joining	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle nucleotide-excision repair complex ERCC4-ERCC1 complex cytoplasm membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle nucleotide-excision repair complex ERCC4-ERCC1 complex cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nucleotide-excision repair factor 1 complex intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region chromosomal region non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A	IPR006167	DNA repair protein XPF	Family
A	IPR010994	RuvA domain 2-like	Homologous Superfamily
A	IPR006166	ERCC4 domain	Domain
A	IPR047520	DNA repair endonuclease XPF, nuclease domain	Domain
B	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
B	IPR010994	RuvA domain 2-like	Homologous Superfamily
B	IPR004579	ERCC1/RAD10/SWI10 family	Family
B	IPR047260	ERCC1-like, central domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q92889	xeroderma pigmentosum Fanconi anemia Fanconi anemia complementation group Q XFE progeroid syndrome xeroderma pigmentosum group F Arsenic Poisoning germ cell tumor urinary bladder cancer peripheral nervous system disease Cockayne syndrome embryonal neoplasm peripheral neuropathy gastric cancer squamous cell carcinoma hematopoietic and lymphoid system neoplasm xeroderma pigmentosum Fanconi anemia Fanconi anemia complementation group Q XFE progeroid syndrome xeroderma pigmentosum group F Arsenic Poisoning germ cell tumor urinary bladder cancer peripheral nervous system disease Cockayne syndrome embryonal neoplasm peripheral neuropathy gastric cancer squamous cell carcinoma hematopoietic and lymphoid system neoplasm inherited disease susceptibility malignant ependymoma aplastic anemia malignant pancreatic neoplasm Cockayne syndrome type 1 osteosarcoma pancreatic ductal adenocarcinoma gastric carcinoma testicular cancer hepatocellular carcinoma intellectual disability melanoma congenital anemia diabetes mellitus ovarian carcinoma esophageal atresia/tracheoesophageal fistula psoriasis skin basal cell carcinoma glioblastoma inherited aplastic anemia urinary bladder neoplasm large cell medulloblastoma xeroderma pigmentosum-Cockayne syndrome complex attention deficit hyperactivity disorder, inattentive type cutaneous melanoma neurofibromatosis type 1 ovarian neoplasm exocrine pancreatic carcinoma
B	Pharos: P07992	cerebrooculofacioskeletal syndrome 4 melanoma nasopharyngeal carcinoma cancer peripheral neuropathy cervical cancer germ cell tumor Arsenic Poisoning non-small cell lung carcinoma peripheral nervous system disease COFS syndrome embryonal neoplasm coloboma testicular cancer gastric cancer cerebrooculofacioskeletal syndrome 4 melanoma nasopharyngeal carcinoma cancer peripheral neuropathy cervical cancer germ cell tumor Arsenic Poisoning non-small cell lung carcinoma peripheral nervous system disease COFS syndrome embryonal neoplasm coloboma testicular cancer gastric cancer inherited disease susceptibility lung carcinoma ovarian cancer Cockayne syndrome type 2 short stature-delayed bone age due to thyroid hormone metabolism deficiency cutaneous melanoma gastric neoplasm xeroderma pigmentosum intellectual disability benign neoplasm cataract pancreatic intraductal papillary-mucinous carcinoma Sjogren syndrome hereditary diffuse gastric adenocarcinoma lung adenocarcinoma medulloblastoma breast cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm Cockayne syndrome

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.