2EXU | pdb_00002exu

Crystal Structure of Saccharomyces cerevisiae transcription elongation factors Spt4-Spt5NGN domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Spt5-NGN	e2exuA4	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	Spt4	e2exuA3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Spt4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.210	Alpha Beta	2-Layer Sandwich	Herpes Virus-1		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
A	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
A	Transcription initiation protein SPT4/SPT5	protein binding binding histone binding RNA binding snRNA binding nucleic acid binding U1 snRNA binding U6 snRNA binding rRNA binding RNA polymerase I core binding RNA polymerase binding RNA polymerase core enzyme binding enzyme binding U4 snRNA binding protein binding binding histone binding RNA binding snRNA binding nucleic acid binding U1 snRNA binding U6 snRNA binding rRNA binding RNA polymerase I core binding RNA polymerase binding RNA polymerase core enzyme binding enzyme binding U4 snRNA binding DNA binding mRNA binding protein-containing complex binding basal transcription machinery binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding U5 snRNA binding transcription factor binding RNA polymerase I general transcription initiation factor binding general transcription initiation factor binding ribonucleoprotein complex binding snRNP binding U2 snRNA binding	ribonucleoprotein complex biogenesis regulation of cellular process RNA metabolic process rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing ribonucleoprotein complex biogenesis regulation of cellular process RNA metabolic process rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process positive regulation of macromolecule biosynthetic process transcription elongation by RNA polymerase I DNA-templated transcription positive regulation of metabolic process transcription by RNA polymerase I rRNA transcription positive regulation of macromolecule metabolic process regulation of DNA-templated transcription elongation regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of transcription elongation by RNA polymerase I regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of RNA biosynthetic process nucleolar large rRNA transcription by RNA polymerase I DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase I positive regulation of RNA biosynthetic process negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of DNA-templated transcription, elongation negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of transcription by RNA polymerase I negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of transcription elongation by RNA polymerase I negative regulation of biosynthetic process mRNA processing protein-RNA complex assembly cellular component organization spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly RNA splicing protein-containing complex organization mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile localization macromolecule localization intracellular mRNA localization RNA localization transcription elongation by RNA polymerase II transcription elongation-coupled chromatin remodeling transcription by RNA polymerase II chromatin organization chromatin remodeling positive regulation of transcription elongation by RNA polymerase II regulation of transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair regulation of cellular response to stress cellular response to stress nucleotide-excision repair response to stress regulation of response to stress DNA repair regulation of transcription-coupled nucleotide-excision repair DNA metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus regulation of nucleotide-excision repair regulation of DNA metabolic process positive regulation of autophagy catabolic process autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process process utilizing autophagic mechanism	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome rDNA heterochromatin heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR041976	Spt5, KOW domain repeat 3	Domain
A	IPR039385	NGN domain, eukaryotic	Domain
A	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
A	IPR022581	Spt5 transcription elongation factor, N-terminal	Domain
A	IPR024945	Spt5 C-terminal domain	Domain
A	IPR006645	NusG-like, N-terminal	Domain
A	IPR041975	Spt5, KOW domain repeat 2	Domain
A	IPR039659	Transcription elongation factor SPT5	Family
A	IPR036735	NusG, N-terminal domain superfamily	Homologous Superfamily
A	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
A	IPR041973	Spt5, KOW domain repeat 1	Domain
A	IPR005100	NGN domain	Domain
A	IPR041977	Spt5, KOW domain repeat 4	Domain
A	IPR017071	Transcription elongation factor Spt5, eukaryote	Family
A	IPR005824	KOW	Domain
A	IPR041978	Spt5, KOW domain repeat 5	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.