2ATW | pdb_00002atw

Structure of a Mycobacterium tuberculosis NusA-RNA 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)
D [auth C]	d2atwc1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	S1 domain of NusA	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D [auth C]	d2atwc2	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	Prokaryotic type KH domain (KH-domain type II)	Prokaryotic type KH domain (KH-domain type II)	Transcription factor NusA, C-terminal domains	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C [auth A]	d2atwa1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	S1 domain of NusA	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C [auth A]	d2atwa2	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	Prokaryotic type KH domain (KH-domain type II)	Prokaryotic type KH domain (KH-domain type II)	Transcription factor NusA, C-terminal domains	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth C]	SCOP2B Superfamily	Prokaryotic type KH domain (KH-domain type II)	8037323	3001043	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Prokaryotic type KH domain (KH-domain type II)	8037322	3001043	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Nucleic acid-binding proteins	8037320	3000135	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleic acid-binding proteins	8037320	3000135	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Prokaryotic type KH domain (KH-domain type II)	8037322	3001043	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Prokaryotic type KH domain (KH-domain type II)	8037323	3001043	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 [auth C]	Stap_Strp_toxin	e2atwC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.1)
D [auth C]	KH_5	e2atwC2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: KH_5	ECOD (v294.1)
D [auth C]	Staphylokinase	e2atwC3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)
C [auth A]	Stap_Strp_toxin	e2atwA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.1)
C [auth A]	KH_5	e2atwA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: KH_5	ECOD (v294.1)
C [auth A]	Staphylokinase	e2atwA3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D [auth C]	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
C [auth A]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C [auth A]	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth C]	PF13184	NusA-like first KH domain (KH_NusA_1st)	NusA-like first KH domain	This entry represents the first K homology (KH) domain found in NusA transcription termination factors. KH domains bind RNA and can function in RNA recognition [1]. NusA binds to RNA polymerase alpha subunit and promotes termination at certain RNA ha ...	This entry represents the first K homology (KH) domain found in NusA transcription termination factors. KH domains bind RNA and can function in RNA recognition [1]. NusA binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures [2]. In prokaryotes, the N-terminal RNA polymerase-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, the S1 and two K-homology (KH), KH1 and KH2. The KH domains of NusA belong to the type II KH RNA-binding domain superfamily [3].	Domain
C [auth A], D [auth C]	PF26594	NusA-like second KH domain (KH_NusA_2nd)	NusA-like second KH domain	This entry represents the second K homology (KH) domain found in NusA transcription termination factors. KH domains bind RNA and can function in RNA recognition [1]. NusA binds to RNA polymerase alpha subunit and promotes termination at certain RNA h ...	This entry represents the second K homology (KH) domain found in NusA transcription termination factors. KH domains bind RNA and can function in RNA recognition [1]. NusA binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures [2]. In prokaryotes, the N-terminal RNA polymerase-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, the S1 and two K-homology (KH), KH1 and KH2. The KH domains of NusA belong to the type II KH RNA-binding domain superfamily [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth C]	Transcription elongation protein nusA	transcription regulator activity DNA-binding transcription factor activity 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane external encapsulating structure extracellular region cell wall peptidoglycan-based cell wall
A [auth B], B [auth D]	ribosomal RNA (5'- AGAACUCAAUAG -3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth C]	IPR036555	NusA, N-terminal domain superfamily	Homologous Superfamily
C [auth A], D [auth C]	IPR003029	S1 domain	Domain
C [auth A], D [auth C]	IPR013735	Transcription factor NusA, N-terminal	Domain
C [auth A], D [auth C]	IPR009019	K homology domain superfamily, prokaryotic type	Homologous Superfamily
C [auth A], D [auth C]	IPR010213	Transcription factor NusA	Domain
C [auth A], D [auth C]	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
C [auth A], D [auth C]	IPR030842	Transcription factor NusA, prokaryotes	Family
C [auth A], D [auth C]	IPR025249	Transcription factor NusA, first KH domain	Domain
C [auth A], D [auth C]	IPR058582	NusA-like, second KH domain	Domain
C [auth A], D [auth C]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

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.