2EXU

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	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Transcription initiation protein SPT4/SPT5	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding rDNA binding protein-containing complex binding basal transcription machinery binding RNA polymerase binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding rDNA binding protein-containing complex binding basal transcription machinery binding RNA polymerase binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 positive regulation of nucleobase-containing compound metabolic process 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 localization cellular localization cellular macromolecule localization macromolecule localization intracellular mRNA localization RNA localization transcription elongation by RNA polymerase II transcription elongation-coupled chromatin remodeling cellular component organization transcription by RNA polymerase II chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic negative regulation of catabolic process catabolic process autophagy regulation of catabolic process regulation of autophagy negative regulation of autophagy process utilizing autophagic mechanism 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 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping mRNA processing mRNA metabolic process RNA 5'-end processing	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF 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 membraneless organelle intracellular membraneless organelle mating-type region heterochromatin chromatin chromosome heterochromatin chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome rDNA heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
A	IPR022800	Spt4/RpoE2 zinc finger	Domain
A	IPR038510	Spt4 superfamily	Homologous Superfamily
A	IPR009287	Transcription initiation Spt4	Family

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.