3MET

Crystal structure of SGF29 in complex with H3K4me2

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DUF1325_C	e3metA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF1325_C	ECOD (1.6)
A	DUF1325_N	e3metA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF1325_N	ECOD (1.6)
B	DUF1325_C	e3metB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF1325_C	ECOD (1.6)
B	DUF1325_N	e3metB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF1325_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07039	SGF29 tudor-like domain (SGF29_Tudor)	SGF29 tudor-like domain	SAGA-associated factor 29 (SGF29) is involved in transcriptional regulation as a chromatin reader component of some histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes [1,2,3,4,5]. It specifically recognises ...	SAGA-associated factor 29 (SGF29) is involved in transcriptional regulation as a chromatin reader component of some histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes [1,2,3,4,5]. It specifically recognises and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for the trimethylated form (H3K4me3). It also may be involved in MYC-mediated oncogenic transformation [1]. This entry represents the two tandem tudor-like domains found at the C-terminal of yeast and human SGF29 proteins and the plant homologues. Each of them has a negatively-charged pocket capable of binding H3A1 and an aromatic cage for the recognition of H3K4me2/3 residues [3,4].	Domain
C, D	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	SAGA-associated factor 29 homolog	methylated histone binding protein binding binding modification-dependent protein binding histone binding methylation-dependent protein binding	regulation of cellular process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II heterocycle metabolic process chromatin organization organic substance biosynthetic process positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of biological process cellular metabolic process regulation of cellular process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II heterocycle metabolic process chromatin organization organic substance biosynthetic process positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of biological process cellular metabolic process regulation of cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of gene expression organic cyclic compound metabolic process biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process protein-DNA complex organization cellular component organization RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process chromatin remodeling nitrogen compound metabolic process cellular component organization or biogenesis positive regulation of cellular process regulation of biosynthetic process protein-containing complex organization epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process heterocycle biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process positive regulation of gene expression cellular process positive regulation of cellular biosynthetic process cellular aromatic compound metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of protein modification process macromolecule deacylation protein deacetylation regulation of protein deacetylation tubulin deacetylation protein metabolic process protein modification process organonitrogen compound metabolic process regulation of protein metabolic process regulation of tubulin deacetylation protein deacylation macromolecule modification positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of nitrogen compound metabolic process positive regulation of RNA biosynthetic process cell division regulation of cell division developmental process multicellular organismal process regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development multicellular organism development anatomical structure development regulation of multicellular organismal process regulation of transcription by RNA polymerase II cell cycle regulation of cell cycle negative regulation of biological process negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process cellular response to stimulus response to stimulus regulation of cellular response to stress cellular response to stress response to stress regulation of response to stress DNA repair DNA metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus regulation of DNA metabolic process RNA processing RNA splicing regulation of RNA splicing protein localization establishment of protein localization cellular localization protein localization to chromatin establishment of protein localization to chromatin establishment of localization localization establishment of protein localization to organelle protein localization to chromosome cellular macromolecule localization macromolecule localization protein localization to organelle establishment of protein localization to chromosome response to endoplasmic reticulum stress	protein-containing complex intracellular anatomical structure catalytic complex peptidase complex protein-DNA complex chromatin chromosome transferase complex cellular anatomical entity histone acetyltransferase complex acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex peptidase complex protein-DNA complex chromatin chromosome transferase complex cellular anatomical entity histone acetyltransferase complex acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex SAGA-type complex SAGA complex intracellular protein-containing complex non-membrane-bounded organelle ATAC complex mitotic spindle cytoskeleton spindle microtubule cytoskeleton membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, D	Histone H3	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR010750	SGF29 tudor-like domain	Domain
A, B	IPR037802	SAGA-associated factor 29	Family
A, B	IPR047287	SAGA-associated factor 29, second Tudor domain	Domain
A, B	IPR047288	SAGA-associated factor 29, first Tudor domain	Domain
C, D	IPR009072	Histone-fold	Homologous Superfamily
C, D	IPR007125	Histone H2A/H2B/H3	Domain
C, D	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q96ES7	allergic rhinitis Chemical and Drug Induced Liver Injury Crohn disease drug-induced liver injury inflammatory bowel disease osteosarcoma attention deficit hyperactivity disorder, inattentive type malignant mesothelioma bipolar disorder chronic obstructive pulmonary disease medulloblastoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	MSE	Parent Component: MET
C, D	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.