5D6Y | pdb_00005d6y

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)
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)
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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J [auth F]	LBR_tudor_1	e5d6yF1	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)
G [auth D]	LBR_tudor_1	e5d6yD1	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)
C [auth B]	LBR_tudor_1	e5d6yB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LBR_tudor_1	ECOD (1.6)
A	LBR_tudor_1	e5d6yA2	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)
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)
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)
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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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 reader activity histone H4K20me2 reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor 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 reader activity histone H4K20me2 reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor 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	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of catabolic process catabolic process autophagy regulation of catabolic process regulation of autophagy negative regulation of autophagy process utilizing autophagic mechanism negative regulation of gene expression muscle hypertrophy multicellular organismal process system process striated muscle adaptation response to stimulus 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 cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome pericentric heterochromatin heterochromatin chromosomal region chromosome, centromeric region nucleolus fibrillar center
B [auth a], D [auth b], F [auth c], H [auth d]	peptide H3K23me3 (19-28)	DNA binding 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 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 biosynthetic process 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 biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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 intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	IPR019787	Zinc finger, 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]	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
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	Core Histone H2A/H2B/H3 domain	Domain
B [auth a], D [auth b], F [auth c], H [auth d]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
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 allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.