5D6Y

Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3

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	Tudor/PWWP/MBT domain-like	8036303	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036304	3000404	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036304	3000404	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036303	3000404	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036303	3000404	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036304	3000404	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036304	3000404	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036303	3000404	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036304	3000404	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036303	3000404	SCOP2B (2022-06-29)
J [auth F]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036304	3000404	SCOP2B (2022-06-29)
J [auth F]	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8036303	3000404	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	LBR_tudor_1	e5d6yA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LBR_tudor_1	ECOD (1.6)
C [auth B]	LBR_tudor_1	e5d6yB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LBR_tudor_1	ECOD (1.6)
E [auth C]	LBR_tudor_1	e5d6yC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LBR_tudor_1	ECOD (1.6)
G [auth D]	LBR_tudor_1	e5d6yD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LBR_tudor_1	ECOD (1.6)
I [auth E]	LBR_tudor_1	e5d6yE2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LBR_tudor_1	ECOD (1.6)
J [auth F]	LBR_tudor_1	e5d6yF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LBR_tudor_1	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)
A	3.10.330.70	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
C [auth B]	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C [auth B]	3.10.330.70	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
E [auth C]	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E [auth C]	3.10.330.70	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
G [auth D]	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G [auth D]	3.10.330.70	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
I [auth E]	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I [auth E]	3.10.330.70	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
J [auth F]	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
J [auth F]	3.10.330.70	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth a], D [auth b], F [auth c], H [auth d]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	PF18104	Jumonji domain-containing protein 2A Tudor domain (Tudor_2)	Jumonji domain-containing protein 2A Tudor domain	This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means o ...	This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms [3]. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD) [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth a], D [auth b], F [auth c], H [auth d]	peptide H3K23me3 (19-28)	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity 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 organic substance metabolic 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 organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	membrane cellular anatomical entity extracellular region 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 membrane cellular anatomical entity extracellular region 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 nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	Lysine-specific demethylase 4A	histone H3K36 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3K36me2/H3K36me3 demethylase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity histone H3K9me2/H3K9me3 demethylase activity histone H3K36 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3K36me2/H3K36me3 demethylase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity histone H3K9me2/H3K9me3 demethylase activity histone H3K9 demethylase activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding methylated histone binding modification-dependent protein binding histone binding methylation-dependent protein binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process multicellular organismal process cellular developmental process regulation of developmental process astrocyte differentiation cell development regulation of cell differentiation regulation of neurogenesis regulation of astrocyte differentiation regulation of gliogenesis regulation of cell development regulation of nervous system development multicellular organism development neurogenesis negative regulation of neurogenesis gliogenesis cell differentiation anatomical structure development regulation of multicellular organismal process negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process regulation of glial cell differentiation nervous system development negative regulation of astrocyte differentiation negative regulation of gliogenesis negative regulation of cell development negative regulation of glial cell differentiation central nervous system development glial cell differentiation negative regulation of multicellular organismal process positive regulation of biological process positive regulation of cellular metabolic 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 gene expression positive regulation of cellular biosynthetic process positive regulation of neuron differentiation positive regulation of developmental process neuron differentiation positive regulation of cell differentiation generation of neurons regulation of neuron differentiation cellular component disassembly chromosome organization cell death cellular component organization execution phase of apoptosis organelle organization apoptotic chromosome condensation chromosome condensation cellular component disassembly involved in execution phase of apoptosis apoptotic nuclear changes apoptotic process cellular component organization or biogenesis programmed cell death negative regulation of cellular catabolic process negative regulation of catabolic process catabolic process autophagy regulation of catabolic process regulation of autophagy cellular catabolic process negative regulation of autophagy regulation of cellular catabolic process process utilizing autophagic mechanism response to nutrient levels response to stimulus negative regulation of gene expression muscle hypertrophy system process striated muscle adaptation striated muscle hypertrophy muscle system process muscle adaptation cardiac muscle adaptation response to stress cardiac muscle hypertrophy cardiac muscle hypertrophy in response to stress muscle hypertrophy in response to stress protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle 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 pericentric heterochromatin heterochromatin chromosomal region chromosome, centromeric region nucleolus fibrillar center

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth a], D [auth b], F [auth c], H [auth d]	IPR009072	Histone-fold	Homologous Superfamily
B [auth a], D [auth b], F [auth c], H [auth d]	IPR007125	Histone H2A/H2B/H3	Domain
B [auth a], D [auth b], F [auth c], H [auth d]	IPR000164	Histone H3/CENP-A	Family
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR001965	Zinc finger, PHD-type	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR002999	Tudor domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR047479	Lysine-specific demethylase 4A, first Tudor domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR003347	JmjC domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR003349	JmjN domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR047481	Lysine-specific demethylase 4A, second Tudor domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR047482	Lysine-specific demethylase 4A, extended PHD finger	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR034732	Extended PHD (ePHD) domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	IPR040477	Lysine-specific demethylase 4-like, Tudor domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth a], D [auth b], F [auth c], H [auth d]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], J [auth F]	Pharos: O75164	attention deficit hyperactivity disorder, inattentive type endogenous depression pancreatic intraductal papillary-mucinous carcinoma autism spectrum disorder medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia bipolar disorder osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth a], D [auth b], F [auth c], H [auth d]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.