6CW3

Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6cw3a_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6cw3c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6cw3b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6cw3b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6cw3d2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6cw3d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth F]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036007	3000403	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036007	3000403	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	V-set_8	e6cw3A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A	C1-set_1	e6cw3A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C	V-set_8	e6cw3C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C	C1-set_1	e6cw3C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B	C1-set_4	e6cw3B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e6cw3B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D	C1-set_4	e6cw3D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D	V-set	e6cw3D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
F [auth E]	Myb_DNA-binding_1	e6cw3E1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Myb_DNA-binding_1	ECOD (1.6)
F [auth E]	ZZ	e6cw3E2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: ZZ	ECOD (1.6)
H [auth G]	Myb_DNA-binding_1	e6cw3G1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Myb_DNA-binding_1	ECOD (1.6)
H [auth G]	ZZ	e6cw3G2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: ZZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A, C	Antibody Fab Fragment	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B, D	Antibody Fab Fragment	L-KAPPA	Homo sapiens (human)	IGKV1D-1301, IGKV1-1302, IGKV1D-1302, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C	Heavy Chain	IGHV3	-	histone acetyltransferase gcn5 \| transcriptional adapter 2	SAbDab (2024-04-19)
B, D	Light Chain	IGKV1	Kappa	histone acetyltransferase gcn5 \| transcriptional adapter 2	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth F], G [auth H]	PF00583	Acetyltransferase (GNAT) family (Acetyltransf_1)	Acetyltransferase (GNAT) family	-	Family
F [auth E], H [auth G]	PF00249	Myb-like DNA-binding domain (Myb_DNA-binding)	Myb-like DNA-binding domain	This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1].	Domain
F [auth E], H [auth G]	PF00569	Zinc finger, ZZ type (ZZ)	Zinc finger, ZZ type	Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	antibody heavy chain	-	-	-
B, D	antibody light chain	-	-	-
E [auth F], G [auth H]	Histone acetyltransferase GCN5	protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding catalytic activity, acting on a protein acyltransferase activity peptide crotonyltransferase activity histone crotonyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding catalytic activity, acting on a protein acyltransferase activity peptide crotonyltransferase activity histone crotonyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity N-acyltransferase activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity N-acetyltransferase activity peptide N-acetyltransferase activity histone acetyltransferase activity acetyltransferase activity peptide-lysine-N-acetyltransferase activity histone H3 acetyltransferase activity	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis chromatin remodeling	protein-containing complex intracellular anatomical structure catalytic 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 protein-containing complex intracellular anatomical structure catalytic 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 intracellular protein-containing complex non-membrane-bounded organelle peptidase complex SAGA-type complex SAGA complex ADA complex cytoplasm cytosol chromosome, centromeric region chromosomal region SLIK (SAGA-like) complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
F [auth E], H [auth G]	Transcriptional adapter 2	protein-containing complex binding chromatin binding binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding protein-containing complex binding chromatin binding binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding modified amino acid binding phospholipid binding lipid binding phosphatidylserine binding	cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process replication-born double-strand break repair via sister chromatid exchange cellular response to stress DNA damage response response to stress cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process replication-born double-strand break repair via sister chromatid exchange cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair subtelomeric heterochromatin formation regulation of cellular process cellular biosynthetic process negative regulation of biological process telomere organization negative regulation of cellular metabolic process cellular component organization protein-DNA complex organization chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation chromosome organization regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organelle organization negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription nucleolar chromatin organization rDNA heterochromatin formation nucleus organization nucleolus organization facultative heterochromatin formation	protein-containing complex intracellular anatomical structure catalytic 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 protein-containing complex intracellular anatomical structure catalytic 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 SLIK (SAGA-like) complex intracellular protein-containing complex non-membrane-bounded organelle peptidase complex SAGA complex ADA complex chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth F], G [auth H]	IPR018359	Bromodomain, conserved site	Conserved Site
E [auth F], G [auth H]	IPR000182	GNAT domain	Domain
E [auth F], G [auth H]	IPR001487	Bromodomain	Domain
E [auth F], G [auth H]	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
E [auth F], G [auth H]	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
E [auth F], G [auth H]	IPR037800	Histone acetyltransferase GCN5	Family
F [auth E], H [auth G]	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
F [auth E], H [auth G]	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
F [auth E], H [auth G]	IPR000433	Zinc finger, ZZ-type	Domain
F [auth E], H [auth G]	IPR041983	ADA2-like, zinc finger, ZZ-type	Domain
F [auth E], H [auth G]	IPR016827	Transcriptional adaptor 2	Family
F [auth E], H [auth G]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F [auth E], H [auth G]	IPR017884	SANT domain	Domain
F [auth E], H [auth G]	IPR001005	SANT/Myb domain	Domain
F [auth E], H [auth G]	IPR007526	SWIRM domain	Domain

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.