Annotations: 9QEC

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8036445	3000163	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Restriction endonuclease-like	8036551	3000104	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8036446	3000163	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02732	ERCC4 domain (ERCC4)	ERCC4 domain	This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase [2-3]. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.	Domain
B	PF00633	Helix-hairpin-helix motif (HHH)	Helix-hairpin-helix motif	-	Motif
B	PF03834	Binding domain of DNA repair protein Ercc1 (rad10/Swi10) (Rad10)	Binding domain of DNA repair protein Ercc1 (rad10/Swi10)	-	Family

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 catalytic activity, acting on a nucleic acid 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 catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA binding damaged DNA binding nucleic acid binding chromatin binding promoter-specific chromatin binding hydrolase activity, acting on ester bonds hydrolase activity 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 meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle DNA recombination organelle fission primary metabolic process DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process cellular process metabolic process macromolecule 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 regulation of primary 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 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 response to light stimulus response to radiation response to abiotic stimulus response to UV UV protection mitotic recombination telomeric DNA-containing double minutes formation telomere maintenance via recombination nucleotide-excision repair involved in interstrand cross-link repair nucleotide-excision repair interstrand cross-link repair DNA repair double-strand break repair recombinational repair double-strand break repair via homologous recombination cellular response to radiation cellular response to environmental stimulus cellular response to light stimulus cellular response to abiotic stimulus cellular response to UV negative regulation of telomere maintenance via telomere lengthening telomere maintenance via telomere lengthening regulation of telomere maintenance via telomere lengthening catabolic process autophagy regulation of catabolic process regulation of autophagy 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 intracellular organelle cellular anatomical structure 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 intracellular organelle cellular anatomical structure 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 membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
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 damaged DNA binding nucleic acid binding chromatin binding promoter-specific 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 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 regulation of primary metabolic process nucleobase-containing 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 primary metabolic process DNA metabolic process regulation of chromosome organization regulation of organelle organization telomere maintenance 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 cellular response to stress response to stress regulation of response to stress negative regulation of cellular 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 replicative senescence cell cycle cell cycle process 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 formation of extrachromosomal circular DNA cellular component biogenesis cellular component assembly telomere maintenance via telomere trimming t-circle formation response to light stimulus response to UV UV protection DNA recombination mitotic recombination telomeric DNA-containing double minutes formation telomere maintenance via recombination positive regulation of organelle organization positive regulation of cellular component organization regulation of t-circle formation positive regulation of biological process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of telomere maintenance positive regulation of cellular component biogenesis regulation of cellular component biogenesis positive regulation of chromosome organization positive regulation of DNA metabolic process positive regulation of t-circle formation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process transcription initiation at RNA polymerase II promoter regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription initiation by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II regulation of macromolecule biosynthetic process regulation of DNA-templated transcription determination of adult lifespan hemopoiesis post-embryonic development post-embryonic hemopoiesis 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 immune system development adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination B cell activation involved in immune response lymphocyte activation cell activation involved in immune response leukocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response leukocyte mediated immunity somatic diversification of immune receptors lymphocyte activation involved in immune response somatic recombination of immunoglobulin genes involved in immune response production of molecular mediator of immune response immune response B cell activation cell activation immunoglobulin mediated immune response adaptive immune response immune effector process somatic diversification of immunoglobulins immune system process somatic diversification of immune receptors via germline recombination within a single locus B cell mediated immunity isotype switching response to oxidative stress multicellular organism growth developmental growth growth pyrimidine dimer repair pyrimidine dimer repair by nucleotide-excision 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 intracellular organelle cellular anatomical structure 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 intracellular organelle cellular anatomical structure 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 membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
C	DNA repair protein complementing XP-A cells	protein binding binding protein domain specific binding DNA binding damaged DNA binding nucleic acid binding identical protein binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding protein binding binding protein domain specific binding DNA binding damaged DNA binding nucleic acid binding identical protein binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding	response to stimulus response to chemical response to toxic substance response to light stimulus response to radiation response to abiotic stimulus response to UV UV protection regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process response to stimulus response to chemical response to toxic substance response to light stimulus response to radiation response to abiotic stimulus response to UV UV protection regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of transcription initiation by RNA polymerase II biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular response to stimulus signaling cell death intracellular signal transduction cell communication apoptotic signaling pathway cellular response to stress DNA damage response response to stress intrinsic apoptotic signaling pathway in response to DNA damage signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death DNA metabolic process nucleotide-excision repair involved in interstrand cross-link repair nucleotide-excision repair interstrand cross-link repair DNA repair base-excision repair nucleotide-excision repair, DNA damage recognition chromosome organization cellular component organization organelle organization cellular component organization or biogenesis 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 catabolic process autophagy regulation of catabolic process regulation of autophagy process utilizing autophagic mechanism response to oxidative stress developmental process multicellular organism growth multicellular organismal process developmental growth growth localization protein localization to organelle macromolecule localization protein localization to nucleus intracellular protein localization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex nuclear protein-containing complex nucleotide-excision repair factor 1 complex nucleotide-excision repair complex intracellular membraneless organelle nuclear body membraneless 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
C	IPR009061	Putative DNA-binding domain superfamily	Homologous Superfamily
C	IPR022656	XPA, C-terminal	Domain
C	IPR022652	Zinc finger, XPA-type, conserved site	Conserved Site
C	IPR000465	XPA/RAD14	Family
C	IPR037129	XPA domain superfamily	Homologous Superfamily
C	IPR022658	XPA, conserved site	Conserved Site

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 aplastic anemia malignant ependymoma 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 urinary bladder neoplasm inherited aplastic anemia xeroderma pigmentosum-Cockayne syndrome complex large cell medulloblastoma 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 COFS syndrome peripheral nervous system disease embryonal neoplasm coloboma gastric cancer testicular cancer cerebrooculofacioskeletal syndrome 4 melanoma nasopharyngeal carcinoma cancer peripheral neuropathy cervical cancer germ cell tumor Arsenic Poisoning non-small cell lung carcinoma COFS syndrome peripheral nervous system disease embryonal neoplasm coloboma gastric cancer testicular cancer inherited disease susceptibility lung carcinoma ovarian cancer Cockayne syndrome type 2 cutaneous melanoma short stature-delayed bone age due to thyroid hormone metabolism deficiency 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 Cockayne syndrome pancreatic intraductal papillary-mucinous neoplasm
C	Pharos: P23025	xeroderma pigmentosum skin basal cell carcinoma skin neoplasm xeroderma pigmentosum group A intestinal cancer liver cancer Micronuclei, Chromosome-Defective skin cancer thyroid gland carcinoma Cockayne syndrome hyperthyroidism melanoma ovarian cancer skin pigmented basal cell carcinoma trichothiodystrophy xeroderma pigmentosum skin basal cell carcinoma skin neoplasm xeroderma pigmentosum group A intestinal cancer liver cancer Micronuclei, Chromosome-Defective skin cancer thyroid gland carcinoma Cockayne syndrome hyperthyroidism melanoma ovarian cancer skin pigmented basal cell carcinoma trichothiodystrophy cutaneous melanoma hypothyroidism intestinal neoplasm liver neoplasm pancreatic intraductal papillary-mucinous neoplasm squamous cell carcinoma Hashimoto thyroiditis intellectual disability malignant mesothelioma osteosarcoma progressive supranuclear palsy

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.