9QEE | pdb_00009qee

Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex

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)
F [auth A]	SCOP2B Superfamily	Helix-hairpin-helix tandem	8036445	3000163	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Helix-hairpin-helix tandem	8036446	3000163	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Restriction endonuclease-like	8036551	3000104	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth 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 [auth C]	PF15744	Uncharacterized protein family UPF0492 (UPF0492)	Uncharacterized protein family UPF0492	-	Family
A [auth B]	PF00633	Helix-hairpin-helix motif (HHH)	Helix-hairpin-helix motif	-	Motif
A [auth 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
F [auth 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
E [auth D]	Structure-specific endonuclease subunit SLX4	DNA binding binding nucleic acid binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	positive regulation of organelle organization regulation of telomere maintenance regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization regulation of t-circle formation positive regulation of biological process telomere organization regulation of primary metabolic process cellular component biogenesis cellular component organization nucleobase-containing compound metabolic process positive regulation of metabolic process cellular component assembly positive regulation of organelle organization regulation of telomere maintenance regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization regulation of t-circle formation positive regulation of biological process telomere organization regulation of primary metabolic process cellular component biogenesis cellular component organization nucleobase-containing compound metabolic process positive regulation of metabolic process cellular component assembly positive regulation of macromolecule metabolic process cellular component organization or biogenesis regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process positive regulation of telomere maintenance formation of extrachromosomal circular DNA positive regulation of cellular component biogenesis biological regulation chromosome organization primary metabolic process DNA metabolic process regulation of chromosome organization regulation of macromolecule metabolic process regulation of cellular component biogenesis nucleic acid metabolic process regulation of organelle organization positive regulation of chromosome organization telomere maintenance organelle organization positive regulation of DNA metabolic process telomere maintenance via telomere trimming t-circle formation cellular process metabolic process positive regulation of t-circle formation macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA replication cellular response to stimulus double-strand break repair response to stimulus DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process meiosis I meiotic nuclear division cell cycle reciprocal homologous recombination cell cycle process meiotic cell cycle organelle fission reciprocal meiotic recombination nuclear division meiosis I cell cycle process negative regulation of telomere maintenance negative regulation of telomere maintenance via telomere lengthening negative regulation of biological process telomere maintenance via telomere lengthening negative regulation of chromosome organization negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of cellular component organization negative regulation of metabolic process regulation of telomere maintenance via telomere lengthening negative regulation of organelle organization negative regulation of DNA metabolic process nucleotide-excision repair DNA double-strand break processing double-strand break repair via single-strand annealing DNA double-strand break processing involved in repair via single-strand annealing response to endogenous stimulus response to intra-S DNA damage checkpoint signaling response to biotic stimulus cellular response to biotic stimulus cellular response to endogenous stimulus response to DNA integrity checkpoint signaling response to DNA damage checkpoint signaling response to cell cycle checkpoint signaling telomeric loop disassembly telomeric D-loop disassembly	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle Slx1-Slx4 complex nuclear lumen chromosome, telomeric region chromosomal region nucleoplasm chromatin
D [auth V]	DNA strand 2	-	-	-
C [auth U]	DNA strand 1	-	-	-
B [auth C]	Protein SLX4IP	-	-	-
A [auth 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth A]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
F [auth A]	IPR006167	DNA repair protein XPF	Family
F [auth A]	IPR010994	RuvA domain 2-like	Homologous Superfamily
F [auth A]	IPR006166	ERCC4 domain	Domain
F [auth A]	IPR047520	DNA repair endonuclease XPF, nuclease domain	Domain
E [auth D]	IPR018574	Structure-specific endonuclease subunit Slx4	Family
E [auth D]	IPR000210	BTB/POZ domain	Domain
E [auth D]	IPR006642	Rad18, zinc finger UBZ4-type	Domain
E [auth D]	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
B [auth C]	IPR031479	Protein SLX4IP	Family
A [auth B]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A [auth B]	IPR010994	RuvA domain 2-like	Homologous Superfamily
A [auth B]	IPR004579	ERCC1/RAD10/SWI10 family	Family
A [auth B]	IPR047260	ERCC1-like, central domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
F [auth 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
E [auth D]	Pharos: Q8IY92	Fanconi anemia Fanconi anemia complementation group P aplastic anemia Esophageal atresia with or without tracheoesophageal fistula hereditary breast carcinoma congenital anemia esophageal atresia/tracheoesophageal fistula inherited aplastic anemia neurofibromatosis type 1 hematopoietic and lymphoid system neoplasm intellectual disability osteosarcoma
B [auth C]	Pharos: Q5VYV7	lung carcinoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor medulloblastoma pancreatic intraductal papillary-mucinous neoplasm subependymal giant cell astrocytoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia tuberculosis
A [auth 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

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.