3PSI | pdb_00003psi

Crystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form Spt6(239-1451)

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	Tex_central_region	e3psiA24	A: alpha bundles	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Tex_central_region	ECOD (develop294)
A	YqgF	e3psiA25	A: alpha bundles	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: YqgF	ECOD (develop294)
A	HHH_7	e3psiA26	A: alpha bundles	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: HHH_7	ECOD (develop294)
A	NAC	e3psiA27	A: alpha bundles	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: NAC	ECOD (develop294)
A	HHH_9	e3psiA6	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: HHH_9	ECOD (develop294)
A	Spt6_S1	e3psiA7	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Spt6_S1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.150.850	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	1.10.10.650	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	RuvA domain 2-like	CATH (4.3.0)
A	1.10.3500.10	Mainly Alpha	Orthogonal Bundle	Tex N-terminal region-like	Tex N-terminal region-like	CATH (4.3.0)
A	3.30.420.140	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.10.10.2740	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Spt6, Death-like domain	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14639	Holliday-junction resolvase-like of SPT6 (YqgF)	Holliday-junction resolvase-like of SPT6	The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC [1] but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage [2]	Domain
A	PF14641	Helix-turn-helix DNA-binding domain of SPT6 (HTH_44)	Helix-turn-helix DNA-binding domain of SPT6	This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.	Domain
A	PF22706	Tex central region-like (Tex_central_region)	Tex central region-like	This domain is found in Tex protein and other related proteins. Tex belongs to a family of prokaryotic transcriptional accessory factors that likely function in a variety of transcriptional processes [1-5].This domain is mainly helical, consisting of ...	This domain is found in Tex protein and other related proteins. Tex belongs to a family of prokaryotic transcriptional accessory factors that likely function in a variety of transcriptional processes [1-5].This domain is mainly helical, consisting of a number of small helices that wrap around a long central helix.	Domain
A	PF21710	Spt6, S1/OB domain (Spt6_S1)	Spt6, S1/OB domain	This entry represents the S1/OB-fold domain of Spt6. This domain has structural similarity to S1 domain but lacks the typical S1 binding cleft residues involved in nucleic acid binding [1], therefore, this domain in Spt6 may be involved in interacti ...	This entry represents the S1/OB-fold domain of Spt6. This domain has structural similarity to S1 domain but lacks the typical S1 binding cleft residues involved in nucleic acid binding [1], therefore, this domain in Spt6 may be involved in interactions with other partners.	Domain
A	PF14635	Helix-hairpin-helix motif (HHH_7)	Helix-hairpin-helix motif		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Transcription elongation factor SPT6	protein binding binding histone binding transcription antitermination factor activity, DNA binding transcription regulator activity DNA binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome 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 mRNA processing RNA 3'-end processing RNA processing regulation of mRNA processing mRNA 3'-end processing regulation of mRNA 3'-end processing mRNA metabolic process regulation of mRNA metabolic process transcription by RNA polymerase II cellular response to stimulus cellular response to stress response to stimulus response to stress protein-DNA complex assembly protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling nucleosome assembly nucleosome organization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport poly(A)+ mRNA export from nucleus intracellular transport establishment of localization RNA export from nucleus establishment of RNA localization macromolecule localization transcription elongation by RNA polymerase II transcription elongation-coupled chromatin remodeling DNA-templated transcription elongation mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription, elongation regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process negative regulation of transcription by RNA polymerase II	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 nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular organelle lumen 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 nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR042066	Spt6, Death-like domain	Homologous Superfamily
A	IPR028231	Transcription elongation factor Spt6, YqgF domain	Domain
A	IPR037027	YqgF/RNase H-like domain superfamily	Homologous Superfamily
A	IPR036860	SH2 domain superfamily	Homologous Superfamily
A	IPR000980	SH2 domain	Domain
A	IPR006641	YqgF/RNase H-like domain	Domain
A	IPR010994	RuvA domain 2-like	Homologous Superfamily
A	IPR023319	Tex-like protein, HTH domain superfamily	Homologous Superfamily
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR017072	Transcription elongation factor Spt6	Family
A	IPR035420	Spt6, SH2 domain	Domain
A	IPR032706	Transcription elongation factor Spt6, helix-hairpin-helix motif	Domain
A	IPR049540	Spt6-like, S1/OB domain	Domain
A	IPR023323	Tex-like domain superfamily	Homologous Superfamily
A	IPR055179	Tex-like, central region	Domain
A	IPR028088	Helix-turn-helix DNA-binding domain of Spt6	Domain
A	IPR035019	Spt6, SH2 domain, N terminus	Domain
A	IPR035018	Spt6, SH2 domain, C terminus	Domain
A	IPR028083	Spt6 acidic, N-terminal domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.