6UBF | pdb_00006ubf

Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth X]	SCOP2B Superfamily	XPC-binding domain	8033589	3000974	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8052789	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-hairpin DNA-binding domain-like	8052785	3002139	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-hairpin DNA-binding domain-like	8052784	3002139	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth X]	ACR_tran	e6ubfX1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ACR_tran	ECOD (v294.1)
A	ACR_tran	e6ubfA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ACR_tran	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth X]	PF09280	XPC-binding domain (XPC-binding)	XPC-binding domain	Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair [1].	Domain
A	PF03835	Rad4 transglutaminase-like domain (Rad4)	Rad4 transglutaminase-like domain		Domain
A	PF10405	Rad4 beta-hairpin domain 3 (BHD_3)	Rad4 beta-hairpin domain 3	This short domain is found in the Rad4 protein. This domain binds to DNA [1].	Domain
A	PF10403	Rad4 beta-hairpin domain 1 (BHD_1)	Rad4 beta-hairpin domain 1	This short domain is found in the Rad4 protein. This domain binds to DNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth Y]	DNA (5'-D(APTPTPGPTPAPGPCPGPGPGPAPTPGPTPCPGPAPGPTPCPA)-3')	-	-	-
C [auth W]	DNA (5'-D(TPTPGPAPCPTPCP(G47)PAPCPAPTPCPCPCGPCPTPAPCPAPA)-3')	-	-	-
B [auth X]	UV excision repair protein RAD23	polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin binding ubiquitin-like protein binding protein-containing complex binding proteasome binding DNA binding damaged DNA binding nucleic acid binding protein-macromolecule adaptor activity molecular adaptor activity	cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress cellular process metabolic process protein metabolic process cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress nucleotide-excision repair, DNA damage recognition chromosome organization DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process organelle organization nucleotide-excision repair DNA damage response cellular component organization or biogenesis DNA repair regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process 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 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 regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex nucleotide-excision repair factor 2 complex nucleotide-excision repair complex catalytic complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex nucleotide-excision repair factor 2 complex nucleotide-excision repair complex catalytic complex peptidase complex PNGase complex cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A	DNA repair protein RAD4	DNA binding binding damaged DNA binding single-strand break-containing DNA binding nucleic acid binding single-stranded DNA binding	cellular response to stimulus mismatch repair response to stimulus 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 metabolic process cellular process macromolecule metabolic process DNA repair cellular response to stimulus mismatch repair response to stimulus 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 metabolic process cellular process macromolecule metabolic process DNA repair nucleotide-excision repair, DNA damage recognition chromosome organization cellular component organization organelle organization nucleotide-excision repair cellular component organization or biogenesis regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process 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 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 regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process DNA conformation change DNA topological change catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle nucleotide-excision repair factor 2 complex intracellular organelle cellular anatomical structure organelle nucleotide-excision repair complex cytoplasm cytosol XPC complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth X]	IPR004806	UV excision repair protein Rad23	Family
B [auth X]	IPR000626	Ubiquitin-like domain	Domain
B [auth X]	IPR036353	XPC-binding domain superfamily	Homologous Superfamily
B [auth X]	IPR015360	XPC-binding domain	Domain
B [auth X]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth X]	IPR009060	UBA-like superfamily	Homologous Superfamily
B [auth X]	IPR015940	Ubiquitin-associated domain	Domain
B [auth X]	IPR006636	Heat shock chaperonin-binding	Domain
A	IPR018326	Rad4 beta-hairpin domain 1	Domain
A	IPR042488	Rad4, beta-hairpin domain 3 superfamily	Homologous Superfamily
A	IPR036985	Transglutaminase-like superfamily	Homologous Superfamily
A	IPR018325	Rad4/PNGase transglutaminase-like fold	Domain
A	IPR004583	DNA repair protein Rad4	Family
A	IPR018328	Rad4 beta-hairpin domain 3	Domain
A	IPR018026	DNA repair protein Rad4-like	Family
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR018327	Rad4 beta-hairpin domain 2	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.