5URN

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65

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	d5urna1	All beta proteins	PH domain-like barrel	PH domain-like	TFIIH domain	RNA polymerase II transcription factor B 73 kDa, TFB1	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d5urna2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PH domain-like	8034115	3000134	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)
A	PH_TFIIH	e5urnA1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH_TFIIH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08567	TFIIH p62 subunit, N-terminal domain (PH_TFIIH)	TFIIH p62 subunit, N-terminal domain	The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision ...	The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal domain reveals that it adopts a pleckstrin homology (PH) fold [1,2]. This PH-type domain has been shown to bind to a mono-phosphorylated inositide [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RNA polymerase II transcription factor B subunit 1	phosphatidylinositol-5-phosphate binding binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding phosphatidylinositol-3-phosphate binding	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process transcription initiation at RNA polymerase II promoter cellular metabolic process cellular nitrogen compound metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process transcription initiation at RNA polymerase II promoter cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair transcription by RNA polymerase I nucleotide-excision repair	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle 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 nucleotide-excision repair factor 3 complex nucleotide-excision repair complex
B	Transcription factor p65	histone deacetylase binding protein binding binding enzyme binding DNA binding organic cyclic compound binding nucleic acid binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding sequence-specific DNA binding double-stranded DNA binding core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding histone deacetylase binding protein binding binding enzyme binding DNA binding organic cyclic compound binding nucleic acid binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding sequence-specific DNA binding double-stranded DNA binding core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding general transcription initiation factor binding ankyrin repeat binding protein domain specific binding ion binding anion binding phosphate ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity kinase binding protein kinase binding transcription coregulator binding transcription coactivator binding protein-containing complex binding chromatin binding chromatin DNA binding DNA-binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding NF-kappaB binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding cytoskeletal protein binding actinin binding peptide binding	response to stimulus response to chemical response to xenobiotic stimulus response to tumor cell defense response response to stress defense response to tumor cell response to biotic stimulus response to ischemia cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation response to stimulus response to chemical response to xenobiotic stimulus response to tumor cell defense response response to stress defense response to tumor cell response to biotic stimulus response to ischemia cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation cell-cell signaling postsynaptic signal transduction cell communication synaptic signaling cellular process postsynapse to nucleus signaling pathway signal transduction cellular response to growth factor stimulus cell surface receptor signaling pathway response to endogenous stimulus cell surface receptor protein tyrosine kinase signaling pathway vascular endothelial growth factor signaling pathway cellular response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus response to growth factor enzyme-linked receptor protein signaling pathway organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process nitrogen compound metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process positive regulation of biological process RNA metabolic process positive regulation of miRNA metabolic process positive regulation of cellular metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process heterocycle metabolic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process cellular nitrogen compound metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process positive regulation of nitrogen compound metabolic process ncRNA metabolic process regulation of metabolic process cellular aromatic compound metabolic process non-canonical NF-kappaB signal transduction intracellular signal transduction intracellular signaling cassette positive regulation of macromolecule biosynthetic process regulation of ncRNA transcription DNA-templated transcription organic substance biosynthetic 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 positive regulation of miRNA transcription RNA biosynthetic process nucleic acid biosynthetic process miRNA transcription positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process ncRNA transcription nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of miRNA transcription response to extracellular stimulus response to nutrient levels response to organic substance response to organonitrogen compound response to nutrient response to oxygen-containing compound response to external stimulus response to nitrogen compound response to vitamin response to cobalamin response to organic cyclic compound multicellular organismal process positive regulation of interleukin-8 production cytokine production regulation of cytokine production regulation of multicellular organismal process interleukin-8 production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production regulation of interleukin-8 production positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway regulation of antigen receptor-mediated signaling pathway regulation of signal transduction positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process regulation of signaling immune response-activating cell surface receptor signaling pathway immune response regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling response to interleukin-6 cellular response to interleukin-6 response to cytokine cellular response to chemical stimulus cellular response to cytokine stimulus cellular response to organic substance biological process involved in interspecies interaction between organisms cellular response to lipoteichoic acid response to other organism response to lipoteichoic acid cellular response to molecule of bacterial origin cellular response to oxygen-containing compound cellular response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin cellular defense response negative regulation of signaling negative regulation of biological process regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process apoptotic process programmed cell death regulation of apoptotic signaling pathway response to organophosphorus response to purine-containing compound response to cAMP negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process cellular aldehyde metabolic process acetaldehyde metabolic process cellular response to interleukin-1 response to interleukin-1 protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis G protein-coupled receptor signaling pathway neuropeptide signaling pathway positive regulation of canonical NF-kappaB signal transduction regulation of intracellular signal transduction positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction developmental process epithelium development epidermis development molting cycle process hair cycle animal organ development tissue development skin development skin epidermis development hair follicle development molting cycle anatomical structure development hair cycle process regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation negative regulation of miRNA transcription negative regulation of miRNA metabolic process cellular response to tumor necrosis factor response to tumor necrosis factor regulation of amide metabolic process amyloid precursor protein catabolic process positive regulation of protein metabolic process regulation of amyloid-beta formation positive regulation of amyloid-beta formation regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process amide metabolic process amyloid precursor protein metabolic process amyloid-beta formation regulation of protein metabolic process positive regulation of amide metabolic process positive regulation of amyloid precursor protein catabolic process cellular response to nicotine response to nicotine response to hormone response to peptide hormone response to insulin regulation of non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction cytokine-mediated signaling pathway interleukin-1-mediated signaling pathway inflammatory response regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis regulation of anatomical structure morphogenesis system development blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process negative regulation of post-translational protein modification regulation of protein sumoylation regulation of protein modification process peptidyl-lysine modification peptidyl-amino acid modification negative regulation of protein modification process protein modification process regulation of protein modification by small protein conjugation or removal negative regulation of protein sumoylation negative regulation of protein metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification protein sumoylation macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of cell adhesion regulation of cell adhesion positive regulation of leukocyte cell-cell adhesion positive regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte adhesion to vascular endothelial cell leukocyte cell-cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion leukocyte adhesion to vascular endothelial cell regulation of leukocyte cell-cell adhesion regulation of cell-cell adhesion response to ketone response to lipid response to progesterone response to steroid hormone response to light stimulus response to radiation response to abiotic stimulus response to UV response to UV-B defense response to symbiont defense response to other organism innate immune response interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production cellular response to nitrogen compound insulin receptor signaling pathway regulation of cellular response to insulin stimulus cellular response to hormone stimulus regulation of insulin receptor signaling pathway cellular response to peptide hormone stimulus negative regulation of cellular response to insulin stimulus cellular response to organonitrogen compound negative regulation of insulin receptor signaling pathway cellular response to insulin stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway innate immune response-activating signaling pathway regulation of innate immune response positive regulation of defense response activation of innate immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus intracellular receptor signaling pathway positive regulation of response to external stimulus regulation of response to stress nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway nucleotide-binding oligomerization domain containing 2 signaling pathway positive regulation of innate immune response regulation of molecular function regulation of DNA-binding transcription factor activity positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity positive regulation of molecular function tumor necrosis factor-mediated signaling pathway negative regulation of protein catabolic process negative regulation of catabolic process regulation of catabolic process regulation of protein catabolic process defense response to virus response to virus positive regulation of transcription by RNA polymerase II hepaticobiliary system development gland development liver development response to acid chemical response to amino acid animal organ morphogenesis cell surface toll-like receptor signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway toll-like receptor 4 signaling pathway response to peptidoglycan cellular response to peptidoglycan regulation of vascular endothelial growth factor production vascular endothelial growth factor production positive regulation of vascular endothelial growth factor production interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production positive regulation of nervous system development cellular developmental process cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis gliogenesis positive regulation of cell differentiation cell differentiation positive regulation of neurogenesis Schwann cell differentiation positive regulation of Schwann cell differentiation positive regulation of cell development regulation of glial cell differentiation peripheral nervous system development nervous system development positive regulation of glial cell differentiation regulation of Schwann cell differentiation glial cell differentiation cellular response to lipopolysaccharide response to lipopolysaccharide cellular response to lipid cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to inorganic substance response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to stress hormone-mediated signaling pathway prolactin signaling pathway regulation of inflammatory response response to muramyl dipeptide response to hepatocyte growth factor cellular response to hepatocyte growth factor stimulus negative regulation of intracellular signal transduction negative regulation of non-canonical NF-kappaB signal transduction response to angiotensin cellular response to angiotensin response to mechanical stimulus response to muscle stretch	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle NF-kappaB complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle protein-DNA complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle NF-kappaB complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle synapse cell junction glutamatergic synapse NF-kappaB p50/p65 complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013876	TFIIH p62 subunit, N-terminal	Domain
A	IPR035925	BSD domain superfamily	Homologous Superfamily
A	IPR027079	TFIIH subunit Tfb1/GTF2H1	Family
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR005607	BSD domain	Domain
B	IPR033926	NFkappaB IPT domain	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR011539	Rel homology domain, DNA-binding domain	Domain
B	IPR030495	Transcription factor p65, RHD domain, N-terminal	Domain
B	IPR002909	IPT domain	Domain
B	IPR030492	Rel homology domain, conserved site	Conserved Site
B	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B	IPR037059	Rel homology domain (RHD), DNA-binding domain superfamily	Homologous Superfamily
B	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
B	IPR000451	NF-kappa-B/Dorsal	Family
B	IPR032397	Rel homology dimerisation domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q04206	renal cell carcinoma ulcerative colitis Barrett esophagus malignant colon neoplasm chronic kidney disease ependymoma cholestasis Neoplasms, Experimental extrahepatic cholestasis skin cancer breast carcinoma chromophobe renal cell carcinoma colitis papillary renal cell carcinoma amphetamine abuse renal cell carcinoma ulcerative colitis Barrett esophagus malignant colon neoplasm chronic kidney disease ependymoma cholestasis Neoplasms, Experimental extrahepatic cholestasis skin cancer breast carcinoma chromophobe renal cell carcinoma colitis papillary renal cell carcinoma amphetamine abuse diabetic peripheral angiopathy hypertensive disorder sarcomatoid renal cell carcinoma brain cancer skin neoplasm type 2 diabetes mellitus collecting duct carcinoma cystitis alcoholic liver cirrhosis plasma cell myeloma brain ischemia mantle cell lymphoma metabolic syndrome X clear cell renal carcinoma colonic neoplasm acne ovarian cancer primary biliary cholangitis heart disease malignant glioma ureteral obstruction maturity-onset diabetes of the young oligodendroglioma astrocytic tumor renal carcinoma cancer medulloblastoma osteoarthritis diabetic kidney disease glioblastoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor benign colon neoplasm ischemia reperfusion injury schizophrenia malignant ependymoma breast cancer

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.