3D3C | pdb_00003d3c

Structural and functional analysis of the E. coli NusB-S10 transcription antitermination 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)
E [auth C]	d3d3cc_	All alpha proteins	NusB-like	NusB-like	Antitermination factor NusB	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth B]	d3d3cb_	All alpha proteins	NusB-like	NusB-like	Antitermination factor NusB	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3d3ca_	All alpha proteins	NusB-like	NusB-like	Antitermination factor NusB	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth L]	SCOP2B Superfamily	Ribosomal protein S10	8102681	3001336	SCOP2B (2022-06-29)
D [auth K]	SCOP2B Superfamily	Ribosomal protein S10	8102681	3001336	SCOP2B (2022-06-29)
B [auth J]	SCOP2B Superfamily	Ribosomal protein S10	8102681	3001336	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	NusB-like	8038005	3000679	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	NusB-like	8038005	3000679	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	NusB-like	8038005	3000679	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)
F [auth L]	IL7	e3d3cL1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
D [auth K]	IL7	e3d3cK1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
B [auth J]	IL7	e3d3cJ1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
E [auth C]	IL7	e3d3cC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
C [auth B]	IL7	e3d3cB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
A	IL7	e3d3cA1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth L]	3.30.70.600	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribosomal protein S10	CATH (4.3.0)
D [auth K]	3.30.70.600	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribosomal protein S10	CATH (4.3.0)
B [auth J]	3.30.70.600	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribosomal protein S10	CATH (4.3.0)
E [auth C]	1.10.940.10	Mainly Alpha	Orthogonal Bundle	N-utilizing Substance Protein B Homolog	Chain A	CATH (4.3.0)
C [auth B]	1.10.940.10	Mainly Alpha	Orthogonal Bundle	N-utilizing Substance Protein B Homolog	Chain A	CATH (4.3.0)
A	1.10.940.10	Mainly Alpha	Orthogonal Bundle	N-utilizing Substance Protein B Homolog	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth J], D [auth K], F [auth L]	PF00338	Ribosomal protein S10p/S20e (Ribosomal_S10)	Ribosomal protein S10p/S20e	This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.	Domain
A, C [auth B], E [auth C]	PF01029	NusB family (NusB)	NusB family	The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth J], D [auth K], F [auth L]	30S ribosomal protein S10	transcription antitermination factor activity, RNA binding transcription regulator activity RNA binding binding tRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process translation protein biosynthetic process cytoplasmic translation protein metabolic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis regulation of DNA-templated transcription elongation DNA-templated transcription elongation	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome membrane-bounded organelle transcription elongation factor complex nucleus protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cytoplasm cytosol cytosolic small ribosomal subunit cytosolic ribosome
A, C [auth B], E [auth C]	N utilization substance protein B	RNA binding binding nucleic acid binding	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth J], D [auth K], F [auth L]	IPR027486	Small ribosomal subunit protein uS10 domain	Domain
B [auth J], D [auth K], F [auth L]	IPR036838	Small ribosomal subunit protein uS10 domain superfamily	Homologous Superfamily
B [auth J], D [auth K], F [auth L]	IPR018268	Small ribosomal subunit protein uS10, conserved site	Conserved Site
B [auth J], D [auth K], F [auth L]	IPR001848	Small ribosomal subunit protein uS10	Family
A, C [auth B], E [auth C]	IPR035926	NusB-like superfamily	Homologous Superfamily
A, C [auth B], E [auth C]	IPR011605	NusB antitermination factor	Family
A, C [auth B], E [auth C]	IPR006027	NusB/RsmB/TIM44	Domain

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.