7CRQ | pdb_00007crq

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G	d7crqg_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
C	d7crqc_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
L	d7crql_	Membrane and cell surface proteins and peptides	SNF-like	SNF-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K [auth I]	d7crqi_	Membrane and cell surface proteins and peptides	SNF-like	SNF-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d7crqh_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	Western clawed frog (Xenopus tropicalis ) [TaxId: 8364 ],	SCOPe (2.08)
D	d7crqd_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	Western clawed frog (Xenopus tropicalis ) [TaxId: 8364 ],	SCOPe (2.08)
F	d7crqf_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
B	d7crqb_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Core histone-like	8070521	3001387	SCOP2B (2022-06-29)
A [auth M]	SCOP2B Superfamily	Core histone-like	8070521	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	e7crqE1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
A [auth M]	e7crqM1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
G	e7crqG1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
C	e7crqC1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
L	e7crqL1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
K [auth I]	e7crqI1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
H	e7crqH1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
D	e7crqD1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
F	e7crqF1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)
B	e7crqB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: V-set	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth M], E	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
C, G	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
K [auth I], L	PF00856	SET domain (SET)	SET domain	-	Family
K [auth I], L	PF17907	AWS domain (AWS)	AWS domain	This entry represents the AWS (associated with SET domain) domain [1]. This is a zinc binding domain. The full AWS domain contains 8 cysteines. This entry represents the N-terminal part of the domain, with the C-terminal part interwoven with the SET ...	This entry represents the AWS (associated with SET domain) domain [1]. This is a zinc binding domain. The full AWS domain contains 8 cysteines. This entry represents the N-terminal part of the domain, with the C-terminal part interwoven with the SET domain.	Domain
B, F	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth M], E	Histone H3	DNA binding 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 intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C, G	Histone H2A	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 epigenetic regulation of gene expression regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
J [auth K]	DNA (168-MER)	-	-	-
K [auth I], L	Histone-lysine N-methyltransferase NSD3	protein-lysine N-methyltransferase activity histone H3K27 trimethyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K27 methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity protein-lysine N-methyltransferase activity histone H3K27 trimethyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K27 methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity molecular function activator activity molecular function regulator activity transcription regulator activator activity histone H3K27 dimethyltransferase activity histone H3K4 methyltransferase activity histone H3K4 dimethyltransferase activity histone H3K36 methyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	methylation metabolic process cellular process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process methylation metabolic process cellular process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process 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 regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome
I [auth A]	DNA (168-MER)	-	-	-
D, H	Histone H2B	DNA binding 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 intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B, F	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth M], E	IPR009072	Histone-fold	Homologous Superfamily
A [auth M], E	IPR000164	Histone H3/CENP-A	Family
A [auth M], E	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, G	IPR009072	Histone-fold	Homologous Superfamily
C, G	IPR002119	Histone H2A	Family
C, G	IPR032454	Histone H2A, C-terminal domain	Domain
C, G	IPR032458	Histone H2A conserved site	Conserved Site
C, G	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
K [auth I], L	IPR006560	AWS domain	Domain
K [auth I], L	IPR047453	Histone-lysine N-methyltransferase NSD3, second PWWP domain	Domain
K [auth I], L	IPR001965	Zinc finger, PHD-type	Domain
K [auth I], L	IPR046341	SET domain superfamily	Homologous Superfamily
K [auth I], L	IPR055197	Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger	Domain
K [auth I], L	IPR001214	SET domain	Domain
K [auth I], L	IPR000313	PWWP domain	Domain
K [auth I], L	IPR041306	NSD, Cys-His rich domain	Domain
K [auth I], L	IPR050777	SET2 Histone-Lysine N-Methyltransferase	Family
K [auth I], L	IPR047527	Histone-lysine N-methyltransferase NSD3, fifth PHD finger	Domain
K [auth I], L	IPR019787	Zinc finger, PHD-finger	Domain
K [auth I], L	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
K [auth I], L	IPR003616	Post-SET domain	Domain
K [auth I], L	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
K [auth I], L	IPR055198	Histone-lysine N-methyltransferase NSD-like, PHD zinc finger	Domain
K [auth I], L	IPR047461	Histone-lysine N-methyltransferase NSD3, SET domain	Domain
K [auth I], L	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
K [auth I], L	IPR047456	Histone-lysine N-methyltransferase NSD3, second PHD finger	Domain
K [auth I], L	IPR047451	Histone-lysine N-methyltransferase NSD3, first PWWP domain	Domain
K [auth I], L	IPR059153	Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1	Domain
K [auth I], L	IPR047458	Histone-lysine N-methyltransferase NSD3, fourth PHD finger	Domain
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR055333	Histone H2B, conserved site	Conserved Site
D, H	IPR000558	Histone H2B	Family
D, H	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B, F	IPR009072	Histone-fold	Homologous Superfamily
B, F	IPR001951	Histone H4	Family
B, F	IPR035425	CENP-T/Histone H4, histone fold	Domain
B, F	IPR019809	Histone H4, conserved site	Conserved Site
B, F	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
K [auth I], L	Pharos: Q9BZ95	pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor Tourette syndrome acute myeloid leukemia autism spectrum disorder cleft lip juvenile dermatomyositis malignant mesothelioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis attention deficit hyperactivity disorder, inattentive type breast cancer glioblastoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor Tourette syndrome acute myeloid leukemia autism spectrum disorder cleft lip juvenile dermatomyositis malignant mesothelioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis attention deficit hyperactivity disorder, inattentive type breast cancer glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease spina bifida atypical teratoid rhabdoid tumor cancer hypertensive disorder malignant glioma myopathy ovarian cancer