4GNG

Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide

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	PHD_5	e4gngA5	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)
A	zf-AN1_like	e4gngA6	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: zf-AN1_like	ECOD (1.6)
C [auth D]	PHD_5	e4gngD5	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)
C [auth D]	zf-AN1_like	e4gngD6	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: zf-AN1_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C [auth D]	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D [auth F]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
A, C [auth D]	PF17982	NSD Cys-His rich domain (C5HCH)	NSD Cys-His rich domain	This is an NSD-specific Cys-His rich region (C5HCH) domain. Family members include NSD3 (nuclear receptor SET domain-containing) proteins. This domain is located on the C-terminal of NSD1, 2 and 3 proteins. C5HCH domain lies adjacent to the fifth pla ...	This is an NSD-specific Cys-His rich region (C5HCH) domain. Family members include NSD3 (nuclear receptor SET domain-containing) proteins. This domain is located on the C-terminal of NSD1, 2 and 3 proteins. C5HCH domain lies adjacent to the fifth plant homeodomain (PHD5). The PHD5-C5HCH module of NSD3 (PHD5-C5HCHNSD3) recognises the H3 N-terminal peptide containing unmodified K4 and trimethylated K9. Moreover, it has been reported that the PHD5-C5HCH module of NSD1 (PHD5-C5HCH) was the sole region required for tight binding of the NUP98-NSD1 fusion protein to the HoxA9 gene promoter, implicating that PHD5-C5HCH might have chromatin targeting ability [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D [auth F]	Histone H3.3	DNA binding protein-containing complex binding binding chromatin binding organic cyclic compound binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding DNA binding protein-containing complex binding binding chromatin binding organic cyclic compound binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 regulation of biological process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth positive regulation of cellular process organelle organization telomere organization chromosome organization	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromosome, telomeric region chromosomal region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, C [auth D]	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 ion binding binding metal ion binding small molecule binding	methylation metabolic process regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process methylation metabolic process regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process 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 regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D [auth F]	IPR009072	Histone-fold	Homologous Superfamily
B, D [auth F]	IPR007125	Histone H2A/H2B/H3	Domain
B, D [auth F]	IPR000164	Histone H3/CENP-A	Family
A, C [auth D]	IPR006560	AWS domain	Domain
A, C [auth D]	IPR047453	Histone-lysine N-methyltransferase NSD3, second PWWP domain	Domain
A, C [auth D]	IPR001965	Zinc finger, PHD-type	Domain
A, C [auth D]	IPR046341	SET domain superfamily	Homologous Superfamily
A, C [auth D]	IPR001214	SET domain	Domain
A, C [auth D]	IPR000313	PWWP domain	Domain
A, C [auth D]	IPR041306	NSD, Cys-His rich domain	Domain
A, C [auth D]	IPR047527	Histone-lysine N-methyltransferase NSD3, fifth PHD finger	Domain
A, C [auth D]	IPR019787	Zinc finger, PHD-finger	Domain
A, C [auth D]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, C [auth D]	IPR003616	Post-SET domain	Domain
A, C [auth D]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A, C [auth D]	IPR047461	Histone-lysine N-methyltransferase NSD3, SET domain	Domain
A, C [auth D]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C [auth D]	IPR047456	Histone-lysine N-methyltransferase NSD3, second PHD finger	Domain
A, C [auth D]	IPR047451	Histone-lysine N-methyltransferase NSD3, first PWWP domain	Domain
A, C [auth D]	IPR047458	Histone-lysine N-methyltransferase NSD3, fourth PHD finger	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D [auth F]	Pharos: P84243	malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer psoriasis astrocytoma (excluding glioblastoma) tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer psoriasis astrocytoma (excluding glioblastoma) tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial intellectual disability lung cancer malignant mesothelioma pituitary cancer subependymal giant cell astrocytoma atopic eczema breast cancer cutaneous lupus erythematosus glioma susceptibility 1 invasive ductal breast carcinoma malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma plasma cell myeloma subependymoma atypical teratoid rhabdoid tumor breast carcinoma Down syndrome exocrine pancreatic carcinoma hepatocellular carcinoma
A, C [auth D]	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