3DOM | pdb_00003dom

Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2

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)
D	d3domd_	Alpha and beta proteins (a+b)	TFB5-like	TFB5-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3domb_	Alpha and beta proteins (a+b)	TFB5-like	TFB5-like	automated matches	automated matches	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)
D	SCOP2B Superfamily	TFB5-like	8086592	3000733	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TFB5-like	8086592	3000733	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)
D		e3domD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F:	ECOD (develop294)
B		e3domB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F:	ECOD (develop294)
C	Tfb2_C	e3domC1	A: alpha bundles	X: Four-helical up-and-down bundle	H: FAD-dependent thiol oxidase	T: FAD-dependent thiol oxidase	F: Tfb2_C	ECOD (develop294)
A		e3domA1	A: alpha bundles	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.70.1220	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	TFB5-like	CATH (4.3.0)
B	3.30.70.1220	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	TFB5-like	CATH (4.3.0)
C	3.30.70.2610	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.70.2610	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF06331	Transcription factor TFIIH complex subunit Tfb5 (Tfb5)	Transcription factor TFIIH complex subunit Tfb5	-	Family
A, C	PF18307	Transcription factor Tfb2 (p52) C-terminal domain (Tfb2_C)	Transcription factor Tfb2 (p52) C-terminal domain	This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH arc ...	This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH architecture and TFIIHs function in nucleotide-excision repair (NER) pathway. The C-terminal domain of Tfb2 is thought to have a crucial role in DNA repair [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	RNA polymerase II transcription factor B subunit 5	-	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 RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process transcription initiation at RNA polymerase II promoter cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization nucleotide-excision repair, preincision complex assembly protein-DNA complex assembly	cellular anatomical structure intracellular anatomical structure cytoplasm 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 cellular anatomical structure intracellular anatomical structure cytoplasm 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 cyclin-dependent protein kinase holoenzyme complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex serine/threonine protein kinase complex RNA polymerase complex nuclear cyclin-dependent protein kinase holoenzyme complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
A, C	RNA polymerase II transcription factor B subunit 2	DNA binding double-stranded DNA binding binding nucleic acid binding ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity	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 RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process transcription initiation at RNA polymerase II promoter	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 intracellular organelle cellular anatomical structure 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 intracellular organelle cellular anatomical structure organelle RNA polymerase II, holoenzyme membrane-enclosed lumen transferase complex intracellular organelle lumen protein kinase complex nucleoplasm transcription factor TFIIH holo complex catalytic complex cyclin-dependent protein kinase holoenzyme complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex serine/threonine protein kinase complex RNA polymerase complex nuclear cyclin-dependent protein kinase holoenzyme complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen nucleotide-excision repair factor 3 complex nucleotide-excision repair complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR009400	TFIIH subunit TTDA/Tfb5	Family
B, D	IPR035935	TFB5-like superfamily	Homologous Superfamily
A, C	IPR040662	Transcription factor Tfb2, C-terminal domain	Domain
A, C	IPR004598	Transcription factor TFIIH subunit p52/Tfb2	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.