8REV

Structure of XPD stalled at a Y-fork DNA containing a interstrand crosslink

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13307	Helicase C-terminal domain (Helicase_C_2)	Helicase C-terminal domain	This domain is found at the C-terminus of DEAD-box helicases.	Domain
A	PF06777	Helical and beta-bridge domain (HBB)	Helical and beta-bridge domain	HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein ...	HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein verifies the presence of damage to DNA and allows DNA repair to proceed. XPD is an assembly of several domains to form a doughnut-shaped molecule that is able to separate two DNA strands and scan the DNA for damage. HBB helps to form the overall DNA-clamping architecture [1]. This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-).	Domain
A	PF06733	DEAD_2 (DEAD_2)	DEAD_2	-	Family
B [auth D]	PF04056	Ssl1-like (Ssl1)	Ssl1-like	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ATP-dependent DNA helicase CHL1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity DNA binding damaged DNA binding nucleic acid binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair regulation of DNA recombination positive regulation of biological process positive regulation of mitotic recombination regulation of mitotic recombination 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 DNA recombination regulation of biological process positive regulation of nucleobase-containing compound metabolic process DNA recombination biological regulation mitotic recombination regulation of macromolecule metabolic process positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
B [auth D]	General transcription and DNA repair factor IIH	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle RNA polymerase II, holoenzyme membrane-enclosed lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle RNA polymerase II, holoenzyme membrane-enclosed lumen transferase complex intracellular organelle lumen protein kinase complex nucleoplasm transcription factor TFIIH holo complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex RNA polymerase complex serine/threonine protein kinase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
C [auth E]	DNA (47-MER)	-	-	-
D [auth B]	DNA (46-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR010643	Helical and beta-bridge domain	Domain
A	IPR006554	Helicase-like, DEXD box c2 type	Domain
A	IPR045028	Helicase superfamily 1/2, DinG/Rad3-like	Family
A	IPR006555	ATP-dependent helicase, C-terminal	Domain
A	IPR010614	RAD3-like helicase, DEAD	Domain
A	IPR002464	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	Conserved Site
A	IPR014013	Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type	Domain
A	IPR001945	RAD3/XPD	Family
A	IPR013020	ATP-dependent helicase Rad3/Chl1-like	Family
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth D]	IPR007198	Ssl1-like	Domain
B [auth D]	IPR012170	TFIIH subunit Ssl1/p44	Family
B [auth D]	IPR004595	TFIIH C1-like domain	Domain
B [auth D]	IPR013087	Zinc finger C2H2-type	Domain
B [auth D]	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B [auth D]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth D]	IPR002035	von Willebrand factor, type A	Domain
B [auth D]	IPR046349	C1-like domain superfamily	Homologous Superfamily

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 R01GM133198.