3LPE | pdb_00003lpe

Crystal structure of Spt4/5NGN heterodimer complex from Methanococcus jannaschii

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)
H	d3lpeh_	Small proteins	Rubredoxin-like	RNA polymerase subunits	automated matches	automated matches	Methanococcus jannaschii (Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
F	d3lpef_	Small proteins	Rubredoxin-like	RNA polymerase subunits	automated matches	automated matches	Methanococcus jannaschii (Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d3lped_	Small proteins	Rubredoxin-like	RNA polymerase subunits	automated matches	automated matches	Methanococcus jannaschii (Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d3lpeb_	Small proteins	Rubredoxin-like	RNA polymerase subunits	automated matches	automated matches	Methanococcus jannaschii (Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	RNA polymerase subunits	8087497	3001823	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RNA polymerase subunits	8087497	3001823	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RNA polymerase subunits	8087497	3001823	SCOP2B (2022-06-29)
B	SCOP2 Family	RpoE2-like	8087496	4003099	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RNA polymerase subunits	8087497	3001823	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)
H	Spt4	e3lpeH1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Spt4	ECOD (1.6)
F	Spt4	e3lpeF1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Spt4	ECOD (1.6)
D	Spt4	e3lpeD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Spt4	ECOD (1.6)
B	Spt4	e3lpeB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Spt4	ECOD (1.6)
G	Spt5-NGN	e3lpeG1	A: a+b two layers	X: Alpha-beta plaits	H: N-utilization substance G protein NusG, N-terminal domain (From Topology)	T: N-utilization substance G protein NusG, N-terminal domain	F: Spt5-NGN	ECOD (1.6)
E	Spt5-NGN	e3lpeE1	A: a+b two layers	X: Alpha-beta plaits	H: N-utilization substance G protein NusG, N-terminal domain (From Topology)	T: N-utilization substance G protein NusG, N-terminal domain	F: Spt5-NGN	ECOD (1.6)
C	Spt5-NGN	e3lpeC1	A: a+b two layers	X: Alpha-beta plaits	H: N-utilization substance G protein NusG, N-terminal domain (From Topology)	T: N-utilization substance G protein NusG, N-terminal domain	F: Spt5-NGN	ECOD (1.6)
A	Spt5-NGN	e3lpeA1	A: a+b two layers	X: Alpha-beta plaits	H: N-utilization substance G protein NusG, N-terminal domain (From Topology)	T: N-utilization substance G protein NusG, N-terminal domain	F: Spt5-NGN	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.20.28.90	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
F	2.20.28.90	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
D	2.20.28.90	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
B	2.20.28.90	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
G	3.30.70.940	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	NusG, N-terminal domain	CATH (4.3.0)
E	3.30.70.940	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	NusG, N-terminal domain	CATH (4.3.0)
C	3.30.70.940	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	NusG, N-terminal domain	CATH (4.3.0)
A	3.30.70.940	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	NusG, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF06093	Spt4/RpoE2 zinc finger (Spt4)	Spt4/RpoE2 zinc finger	This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via ...	This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles [1]. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in [3]. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery.	Domain
A, C, E, G	PF03439	Early transcription elongation factor of RNA pol II, NGN section (Spt5-NGN)	Early transcription elongation factor of RNA pol II, NGN section	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	DNA-directed RNA polymerase subunit E''	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-
A, C, E, G	Putative transcription antitermination protein nusG	translation factor activity translation elongation factor activity structural molecule activity structural constituent of ribosome	transcription elongation by RNA polymerase II transcription elongation-coupled chromatin remodeling RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II transcription elongation by RNA polymerase II transcription elongation-coupled chromatin remodeling RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II biosynthetic process chromatin organization chromatin remodeling cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process regulation of DNA-templated transcription elongation	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR038589	Transcription elongation factor Spt4 superfamily, archaea	Homologous Superfamily
B, D, F, H	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
B, D, F, H	IPR007178	Transcription elongation factor Spt4, archaea	Family
B, D, F, H	IPR022800	Spt4/RpoE2 zinc finger	Domain
A, C, E, G	IPR036735	NusG, N-terminal domain superfamily	Homologous Superfamily
A, C, E, G	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
A, C, E, G	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR005100	NGN domain	Domain
A, C, E, G	IPR011590	Transcription elongation factor Spt5, archaeal	Family
A, C, E, G	IPR005824	KOW	Domain
A, C, E, G	IPR006645	NusG-like, N-terminal	Domain
A, C, E, G	IPR039659	Transcription elongation factor SPT5	Family
A, C, E, G	IPR005825	Large ribosomal subunit protein uL24, conserved site	Conserved Site

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.