1JFI

Crystal Structure of the NC2-TBP-DNA Ternary Complex

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1jfia_	All alpha proteins	Histone-fold	Histone-fold	TBP-associated factors, TAFs	Negative cofactor 2, NC2, alpha chain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d1jfib_	All alpha proteins	Histone-fold	Histone-fold	TBP-associated factors, TAFs	Negative cofactor 2, NC2, beta chain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d1jfic1	Alpha and beta proteins (a+b)	TBP-like	TATA-box binding protein-like	TATA-box binding protein (TBP), C-terminal domain	TATA-box binding protein (TBP), C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d1jfic3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	TBP-associated factors TAFs	8022009	4000797	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Core histone-like	8034389	3001387	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Family	TBP-associated factors TAFs	8022013	4000797	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	Core histone-like	8034393	3001387	SCOP2 (2022-06-29)
E [auth C]	SCOP2B Superfamily	TATA-box binding protein-like	8036295	3000705	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	TATA-box binding protein-like	8036293	3000705	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)
C [auth A]	PF00808	e1jfiA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00808	ECOD (1.6)
D [auth B]	PF00808	e1jfiB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00808	ECOD (1.6)
E [auth C]	PF00352	e1jfiC1	A: a+b two layers	X: TBP-like	H: TATA-box binding protein-like (From Topology)	T: TATA-box binding protein-like	F: PF00352	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
D [auth B]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
E [auth C]	3.30.310.10	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	TATA-Binding Protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF00808	Histone-like transcription factor (CBF/NF-Y) and archaeal histone (CBFD_NFYB_HMF)	Histone-like transcription factor (CBF/NF-Y) and archaeal histone	This family includes archaebacterial histones and histone like transcription factors from eukaryotes.	Domain
D [auth B]	PF00808	Histone-like transcription factor (CBF/NF-Y) and archaeal histone (CBFD_NFYB_HMF)	Histone-like transcription factor (CBF/NF-Y) and archaeal histone	This family includes archaebacterial histones and histone like transcription factors from eukaryotes.	Domain
E [auth C]	PF00352	Transcription factor TFIID (or TATA-binding protein, TBP) (TBP)	Transcription factor TFIID (or TATA-binding protein, TBP)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A]	Transcription Regulator NC2 alpha chain	transcription factor binding protein binding binding TBP-class protein binding general transcription initiation factor binding protein heterodimerization activity protein dimerization activity general transcription initiation factor activity RNA polymerase II general transcription initiation factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription factor binding protein binding binding TBP-class protein binding general transcription initiation factor binding protein heterodimerization activity protein dimerization activity general transcription initiation factor activity RNA polymerase II general transcription initiation factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding basal transcription machinery binding basal RNA polymerase II transcription machinery binding RNA polymerase II general transcription initiation factor binding identical protein 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 organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic 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 regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression 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 negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle RNA polymerase II transcription repressor complex transcription repressor complex negative cofactor 2 complex
D [auth B]	Transcription Regulator NC2 beta chain	DNA binding binding organic cyclic compound binding nucleic acid binding transcription factor binding protein binding TBP-class protein binding general transcription initiation factor binding protein heterodimerization activity protein dimerization activity general transcription initiation factor activity RNA polymerase II general transcription initiation factor activity	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process transcription preinitiation complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly transcription by RNA polymerase II protein-containing complex assembly cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter protein-containing complex organization protein-DNA complex assembly DNA-templated transcription initiation RNA polymerase II preinitiation complex assembly organonitrogen compound metabolic process regulation of protein modification process regulation of protein metabolic process macromolecule deacylation protein deacetylation regulation of tubulin deacetylation protein deacylation regulation of protein deacetylation tubulin deacetylation macromolecule modification protein metabolic process protein modification process cell division regulation of cell division developmental process multicellular organismal process regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development multicellular organism development anatomical structure development regulation of multicellular organismal process regulation of transcription by RNA polymerase II cell cycle regulation of cell cycle negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process 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 cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle catalytic complex protein-DNA complex ATAC complex RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle catalytic complex protein-DNA complex ATAC complex chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular non-membrane-bounded organelle protein acetyltransferase complex SAGA-type complex intracellular protein-containing complex non-membrane-bounded organelle mitotic spindle cytoskeleton spindle microtubule cytoskeleton RNA polymerase II transcription repressor complex transcription repressor complex negative cofactor 2 complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
E [auth C]	TATA-BOX-BINDING PROTEIN (TBP)	transcription factor binding basal transcription machinery binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding TFIIB-class transcription factor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding transcription factor binding basal transcription machinery binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding TFIIB-class transcription factor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding core promoter sequence-specific DNA binding RNA polymerase III general transcription initiation factor activity general transcription initiation factor activity DNA-binding transcription factor binding RNA polymerase II general transcription initiation factor activity RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II-specific DNA-binding transcription factor binding signaling receptor binding aryl hydrocarbon receptor binding enzyme binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular biosynthetic process transcription preinitiation complex assembly RNA metabolic process cellular component organization cellular component biogenesis protein-DNA complex organization developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular biosynthetic process transcription preinitiation complex assembly RNA metabolic process cellular component organization cellular component biogenesis protein-DNA complex organization RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process cellular component assembly organic substance metabolic process transcription by RNA polymerase II protein-containing complex assembly organic substance biosynthetic process cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter protein-containing complex organization cellular metabolic process protein-DNA complex assembly primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process RNA polymerase II preinitiation complex assembly cellular process metabolic process macromolecule metabolic process regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of transcription initiation by RNA polymerase II biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II positive regulation of cellular biosynthetic process mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase III	RNA polymerase II transcription regulator complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex RNA polymerase II transcription regulator complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex transcription factor TFIIA complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen transcription factor TFIID complex cytoplasm protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle pronucleus male pronucleus female pronucleus RNA polymerase transcription factor SL1 complex nucleolus RNA polymerase I transcription regulator complex euchromatin germ cell nucleus female germ cell nucleus male germ cell nucleus
A [auth D]	5'-D(TPTPGPGPCPTPAPTPAPAPAPAPGPGPGPCPTPCP*C)-3'	-	-	-
B [auth E]	5'-D(GGPAPGPCPCPCPTPTPTPTPAPTPAPGPCPCPAP*A)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR009072	Histone-fold	Homologous Superfamily
C [auth A]	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain	Domain
D [auth B]	IPR009072	Histone-fold	Homologous Superfamily
D [auth B]	IPR042225	Negative cofactor 2 complex subunit beta	Family
D [auth B]	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain	Domain
E [auth C]	IPR030491	TATA-box binding protein, conserved site	Conserved Site
E [auth C]	IPR000814	TATA-box binding protein	Family
E [auth C]	IPR012295	TBP domain superfamily	Homologous Superfamily
E [auth C]	IPR033710	TATA-box binding protein, eukaryotic	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: Q14919	melanoma congestive heart failure inflammatory bowel disease skin basal cell carcinoma Crohn disease type 2 diabetes mellitus cutaneous melanoma rheumatoid arthritis
D [auth B]	Pharos: Q01658	atypical teratoid rhabdoid tumor exocrine pancreatic carcinoma lung cancer malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sarcoidosis breast cancer glioblastoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm ovarian cancer plasma cell myeloma Sjogren syndrome cystic fibrosis atypical teratoid rhabdoid tumor exocrine pancreatic carcinoma lung cancer malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sarcoidosis breast cancer glioblastoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm ovarian cancer plasma cell myeloma Sjogren syndrome cystic fibrosis large cell medulloblastoma malignant glioma metabolic syndrome X pancreatic intraductal papillary-mucinous carcinoma psoriasis
E [auth C]	Pharos: P20226	spinocerebellar ataxia type 17 autosomal dominant cerebellar ataxia late-onset Parkinson disease Parkinson disease acute myeloid leukemia hereditary ataxia malignant mesothelioma osteosarcoma psoriasis Ataxias, Hereditary intellectual disability medulloblastoma ovarian cancer schizophrenia neurodegenerative disease

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.