Annotations: 5LM9

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Rad51 N-terminal domain-like	8040765	3000529	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)
A	S1_3	e5lm9A4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_3	ECOD (1.6)
A	HHH_5	e5lm9A1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
A	KH_5	e5lm9A2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_5	ECOD (1.6)
A	nusA	e5lm9A3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: nusA	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
A	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Transcription termination/antitermination protein NusA	protein binding binding protein domain specific binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA polymerase binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding transcription regulator activity DNA-binding transcription factor activity RNA binding protein binding binding protein domain specific binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA polymerase binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding transcription regulator activity DNA-binding transcription factor activity RNA binding nucleic acid binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis 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 cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis 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 nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process 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 ribosome biogenesis ribonucleoprotein complex biogenesis regulation of DNA-templated transcription elongation DNA-templated transcription elongation	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036555	NusA, N-terminal domain superfamily	Homologous Superfamily
A	IPR003029	S1 domain	Domain
A	IPR013735	Transcription factor NusA, N-terminal	Domain
A	IPR009019	K homology domain superfamily, prokaryotic type	Homologous Superfamily
A	IPR010214	Transcription termination factor NusA, C-terminal duplication	Repeat
A	IPR010213	Transcription factor NusA	Domain
A	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
A	IPR025249	Transcription factor NusA, first KH domain	Domain
A	IPR030842	Transcription factor NusA, prokaryotes	Family
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR010995	DNA repair Rad51/transcription factor NusA, alpha-helical	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.