4WZS | pdb_00004wzs

Crystal structure of the Mot1 N-terminal domain in complex with TBP and NC2 bound to a promoter DNA fragment

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	TBP-associated factors, TAFs	8084161	4000797	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Core histone-like	8084162	3001387	SCOP2 (2022-06-29)
A	SCOP2 Family	TBP-associated factors, TAFs	8084793	4000797	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Core histone-like	8084794	3001387	SCOP2 (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	TBP	e4wzsD2	A: a+b two layers	X: TBP-like	H: TATA-box binding protein-like (From Topology)	T: TATA-box binding protein-like	F: TBP	ECOD (1.6)
C	CLASP_N_2	e4wzsC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CLASP_N_2	ECOD (1.6)
B	CBFD_NFYB_HMF	e4wzsB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: CBFD_NFYB_HMF	ECOD (1.6)
A	CBFD_NFYB_HMF	e4wzsA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: CBFD_NFYB_HMF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	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
F	DNA (5'-D(PGPGPGPCPTPAPTPAPAPAPAPGPGPGPGPGPTPGP*G)-3')	-	-	-
E	DNA (5'-D(PCPCPAPCPCPCPCPCPTPTPTPTPAPTPAPGPCPCPCPT)-3')	-	-	-
D	ECU04_1440 protein	DNA binding binding nucleic acid binding identical protein binding protein binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation 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 transcription initiation at RNA polymerase II promoter	protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
C	Similarity to HELICASE MOT1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity transcription factor binding protein binding TBP-class protein binding general transcription initiation factor binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides identical protein binding	-	-
B	TATA-binding protein-associated phosphoprotein	protein heterodimerization activity protein binding binding protein dimerization activity general transcription initiation factor activity RNA polymerase II general transcription initiation factor activity transcription factor binding TBP-class protein binding general transcription initiation factor 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 transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic 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 transcription by RNA polymerase II 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 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 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 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	membrane-bounded organelle RNA polymerase II transcription repressor complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle transcription repressor complex negative cofactor 2 complex
A	ECU11_1470 protein	protein heterodimerization activity protein binding binding 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 core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR030491	TATA-box binding protein, conserved site	Conserved Site
D	IPR000814	TATA-box binding protein	Family
D	IPR012295	TBP domain superfamily	Homologous Superfamily
D	IPR033710	TATA-box binding protein, eukaryotic	Family
C	IPR000330	SNF2, N-terminal	Domain
C	IPR016024	Armadillo-type fold	Homologous Superfamily
C	IPR001650	Helicase, C-terminal domain-like	Domain
C	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
C	IPR011989	Armadillo-like helical	Homologous Superfamily
C	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
C	IPR044972	TATA-binding protein-associated factor Mot1	Family
C	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain	Domain
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR042225	Negative cofactor 2 complex subunit beta	Family
A	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain	Domain
A	IPR009072	Histone-fold	Homologous Superfamily
A	IPR050568	Transcription/DNA replication regulator	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.