1NGM | pdb_00001ngm

Crystal structure of a yeast Brf1-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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
P [auth N]	d1ngmn_	Peptides	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
N [auth J]	d1ngmj_	Peptides	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
L [auth F]	d1ngmf1	Peptides	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
L [auth F]	d1ngmf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J [auth B]	d1ngmb1	Peptides	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	TBP-binding domain of the transcription factor IIIb Brf1 subunit	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J [auth B]	d1ngmb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
O [auth M]	d1ngmm1	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
M [auth I]	d1ngmi1	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
K [auth E]	d1ngme1	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
I [auth A]	d1ngma1	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
O [auth M]	SCOP2B Superfamily	TATA-box binding protein-like	8036831	3000705	SCOP2B (2022-06-29)
O [auth M]	SCOP2B Superfamily	TATA-box binding protein-like	8036833	3000705	SCOP2B (2022-06-29)
M [auth I]	SCOP2B Superfamily	TATA-box binding protein-like	8036833	3000705	SCOP2B (2022-06-29)
M [auth I]	SCOP2B Superfamily	TATA-box binding protein-like	8036831	3000705	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	TATA-box binding protein-like	8036833	3000705	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	TATA-box binding protein-like	8036831	3000705	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	TATA-box binding protein-like	8036831	3000705	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	TATA-box binding protein-like	8036833	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)
J [auth B]		e1ngmB01	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (v294.1)
O [auth M]	Polyketide_cyc2	e1ngmM1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Polyketide_cyc2	ECOD (v294.1)
M [auth I]	Polyketide_cyc2	e1ngmI1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Polyketide_cyc2	ECOD (v294.1)
K [auth E]	Polyketide_cyc2	e1ngmE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Polyketide_cyc2	ECOD (v294.1)
I [auth A]	Polyketide_cyc2	e1ngmA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Polyketide_cyc2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P [auth N]	1.20.5.650	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
N [auth J]	1.20.5.650	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
L [auth F]	1.20.5.650	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
J [auth B]	1.20.5.650	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
O [auth M]	3.30.310.10	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	TATA-Binding Protein	CATH (4.3.0)
M [auth I]	3.30.310.10	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	TATA-Binding Protein	CATH (4.3.0)
K [auth E]	3.30.310.10	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	TATA-Binding Protein	CATH (4.3.0)
I [auth A]	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
J [auth B], L [auth F], N [auth J], P [auth N]	PF07741	Brf1-like TBP-binding domain (BRF1)	Brf1-like TBP-binding domain	In budding yeasts, Brf1 forms the TFIIIB complex with TATA-binding protein (TBP) and Bdp1 [1]. The TFIIIB complex can be recruited to the Pol III promoters and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol I ...	In budding yeasts, Brf1 forms the TFIIIB complex with TATA-binding protein (TBP) and Bdp1 [1]. The TFIIIB complex can be recruited to the Pol III promoters and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol III enzymatic complex and helps maintain it for multiple transcription cycles in a process called facilitated recycling [2]. This entry represents the TATA binding protein (TBP) binding domain of Brf1 that covers both the Brf homology II and III regions [3].	Domain
I [auth A], K [auth E], M [auth I], O [auth M]	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
J [auth B], L [auth F], N [auth J], P [auth N]	Transcription factor IIIB BRF1 subunit	DNA binding binding nucleic acid binding RNA polymerase binding protein binding RNA polymerase core enzyme binding enzyme binding RNA polymerase III core binding RNA polymerase III type 3 promoter sequence-specific DNA binding sequence-specific DNA binding RNA polymerase III transcription regulatory region sequence-specific DNA binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding DNA binding binding nucleic acid binding RNA polymerase binding protein binding RNA polymerase core enzyme binding enzyme binding RNA polymerase III core binding RNA polymerase III type 3 promoter sequence-specific DNA binding sequence-specific DNA binding RNA polymerase III transcription regulatory region sequence-specific DNA binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding RNA polymerase III cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription factor binding TFIIIC-class transcription factor complex binding RNA polymerase III general transcription initiation factor binding general transcription initiation factor binding RNA polymerase III general transcription initiation factor activity general transcription initiation factor activity TBP-class protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process transcription by RNA polymerase III regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase III regulation of biological process regulation of cellular process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process transcription by RNA polymerase III regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase III regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process DNA-templated transcription initiation transcription preinitiation complex assembly RNA polymerase III preinitiation complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis transcription initiation at RNA polymerase III promoter protein-containing complex organization protein-DNA complex assembly protein-DNA complex remodeling DNA-templated transcription open complex formation protein-containing complex remodeling	transcription preinitiation complex protein-containing complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle transcription preinitiation complex protein-containing complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen RNA polymerase III transcription regulator complex transcription factor TFIIIB complex transcription regulator complex
I [auth A], K [auth E], M [auth I], O [auth M]	Transcription initiation factor TFIID	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding chromatin binding RNA polymerase binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme binding RNA polymerase II general transcription initiation factor binding TFIIA-class transcription factor complex binding RNA polymerase III transcription regulatory region sequence-specific DNA binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding chromatin binding RNA polymerase binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme binding RNA polymerase II general transcription initiation factor binding TFIIA-class transcription factor complex binding RNA polymerase III transcription regulatory region sequence-specific DNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA polymerase I general transcription initiation factor binding DNA binding, bending general transcription initiation factor activity RNA polymerase II general transcription initiation factor activity 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 disordered domain specific binding protein domain specific binding	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 nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process 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 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 nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process 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 negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA 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 transcription by RNA polymerase III regulation of transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process RNA polymerase I preinitiation complex assembly transcription initiation at RNA polymerase I promoter RNA polymerase III preinitiation complex assembly transcription initiation at RNA polymerase III promoter positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	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 cellular anatomical structure nucleoplasm 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 cellular anatomical structure nucleoplasm catalytic complex intracellular membrane-bounded organelle 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 RNA polymerase III transcription regulator complex transcription factor TFIIIB complex
B [auth D], D [auth H], F [auth L], H [auth P]	5'-D(APAPAPAPAPAPCPAPTPTPTPTPTPTPTPAPTPAP*G)-3'	-	-	-
A [auth C], C [auth G], E [auth K], G [auth O]	5'-D(CPTPAPTPAPAPAPAPAPAPAPTPGPTPTPTPTPTP*T)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
J [auth B], L [auth F], N [auth J], P [auth N]	IPR000812	Transcription factor TFIIB	Family
J [auth B], L [auth F], N [auth J], P [auth N]	IPR023486	Transcription factor TFIIB, conserved site	Conserved Site
J [auth B], L [auth F], N [auth J], P [auth N]	IPR011665	Brf1, TBP-binding domain	Domain
J [auth B], L [auth F], N [auth J], P [auth N]	IPR013150	Transcription factor TFIIB, cyclin-like domain	Domain
J [auth B], L [auth F], N [auth J], P [auth N]	IPR013137	Zinc finger, TFIIB-type	Domain
J [auth B], L [auth F], N [auth J], P [auth N]	IPR036915	Cyclin-like superfamily	Homologous Superfamily
J [auth B], L [auth F], N [auth J], P [auth N]	IPR013763	Cyclin-like domain	Domain
I [auth A], K [auth E], M [auth I], O [auth M]	IPR030491	TATA-box binding protein, conserved site	Conserved Site
I [auth A], K [auth E], M [auth I], O [auth M]	IPR000814	TATA-box binding protein	Family
I [auth A], K [auth E], M [auth I], O [auth M]	IPR012295	TBP domain superfamily	Homologous Superfamily
I [auth A], K [auth E], M [auth I], O [auth M]	IPR033710	TATA-box binding protein, eukaryotic	Family

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.