4L1U | pdb_00004l1u

Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Plus3-like	8033751	3000248	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Plus3-like	8033751	3000248	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Plus3-like	8033751	3000248	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Plus3-like	8033751	3000248	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Plus3-like	8033751	3000248	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Plus3-like	8033751	3000248	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	Plus-3	e4l1uA1	A: beta barrels	X: SH3	H: Plus3 (From Topology)	T: Plus3	F: Plus-3	ECOD (1.6)
B	Plus-3	e4l1uB1	A: beta barrels	X: SH3	H: Plus3 (From Topology)	T: Plus3	F: Plus-3	ECOD (1.6)
C	Plus-3	e4l1uC1	A: beta barrels	X: SH3	H: Plus3 (From Topology)	T: Plus3	F: Plus-3	ECOD (1.6)
E	Plus-3	e4l1uE1	A: beta barrels	X: SH3	H: Plus3 (From Topology)	T: Plus3	F: Plus-3	ECOD (1.6)
F	Plus-3	e4l1uF1	A: beta barrels	X: SH3	H: Plus3 (From Topology)	T: Plus3	F: Plus-3	ECOD (1.6)
D	Plus-3	e4l1uD1	A: beta barrels	X: SH3	H: Plus3 (From Topology)	T: Plus3	F: Plus-3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.70.200	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B	3.90.70.200	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C	3.90.70.200	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
E	3.90.70.200	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
F	3.90.70.200	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
D	3.90.70.200	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF03126	Plus-3 domain (Plus-3)	Plus-3 domain	This domain is about 90 residues in length and is often found associated with the Pfam:PF02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged ...	This domain is about 90 residues in length and is often found associated with the Pfam:PF02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	RNA polymerase-associated protein RTF1 homolog	RNA binding binding nucleic acid binding DNA binding single-stranded DNA binding	developmental process multicellular organismal process maintenance of cell number stem cell population maintenance transcription elongation by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription developmental process multicellular organismal process maintenance of cell number stem cell population maintenance transcription elongation by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process 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 metabolic process cellular process macromolecule metabolic process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication signal transduction Wnt signaling pathway negative regulation of biological process regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of macromolecule metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process formation of primary germ layer cellular developmental process embryonic morphogenesis embryo development tissue development gastrulation cell fate commitment involved in formation of primary germ layer anatomical structure morphogenesis multicellular organism development endoderm development cell differentiation anatomical structure formation involved in morphogenesis anatomical structure development endoderm formation cell fate commitment endodermal cell fate commitment endodermal cell differentiation developmental growth chordate embryonic development growth in utero embryonic development embryo development ending in birth or egg hatching blastocyst growth blastocyst development cellular component organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nuclear protein-containing complex transferase complex nucleoplasm catalytic complex Cdc73/Paf1 complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex
G, H, I, J	Transcription elongation factor SPT5	chromatin binding binding protein heterodimerization activity protein binding protein dimerization activity RNA binding nucleic acid binding mRNA binding enzyme binding	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation 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 positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of DNA-templated transcription, elongation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process transcription elongation by RNA polymerase II transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of autophagy catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process regulation of macroautophagy positive regulation of macroautophagy process utilizing autophagic mechanism transcription elongation-coupled chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis positive regulation of transcription elongation by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036128	Plus3-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR004343	Plus-3 domain	Domain
G, H, I, J	IPR041976	Spt5, KOW domain repeat 3	Domain
G, H, I, J	IPR041980	Spt5, KOW domain repeat 6, metazoa	Domain
G, H, I, J	IPR039385	NGN domain, eukaryotic	Domain
G, H, I, J	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
G, H, I, J	IPR022581	Spt5 transcription elongation factor, N-terminal	Domain
G, H, I, J	IPR024945	Spt5 C-terminal domain	Domain
G, H, I, J	IPR006645	NusG-like, N-terminal	Domain
G, H, I, J	IPR041975	Spt5, KOW domain repeat 2	Domain
G, H, I, J	IPR039659	Transcription elongation factor SPT5	Family
G, H, I, J	IPR036735	NusG, N-terminal domain superfamily	Homologous Superfamily
G, H, I, J	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
G, H, I, J	IPR041973	Spt5, KOW domain repeat 1	Domain
G, H, I, J	IPR005100	NGN domain	Domain
G, H, I, J	IPR041977	Spt5, KOW domain repeat 4	Domain
G, H, I, J	IPR017071	Transcription elongation factor Spt5, eukaryote	Family
G, H, I, J	IPR005824	KOW	Domain
G, H, I, J	IPR041978	Spt5, KOW domain repeat 5	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: Q92541	allergic rhinitis ovarian cancer metabolic syndrome X osteosarcoma
G, H, I, J	Pharos: O00267	diabetes mellitus ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I, J	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.