3QLA

Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
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	ADDz_ATRX	e3qlaA3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_ATRX	ECOD (1.6)
A	ADDz_Dnmt3b	e3qlaA2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_Dnmt3b	ECOD (1.6)
C [auth D]	ADDz_ATRX	e3qlaD2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_ATRX	ECOD (1.6)
C [auth D]	ADDz_Dnmt3b	e3qlaD1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_Dnmt3b	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D]	PF17981	Cysteine Rich ADD domain (ADD_ATRX)	Cysteine Rich ADD domain	This is a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in ATRX proteins. Chromatin-associated human protein ATRX was originally identified because mutations in the ATRX gene cause a severe form of syndromal X-linked mental reta ...	This is a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in ATRX proteins. Chromatin-associated human protein ATRX was originally identified because mutations in the ATRX gene cause a severe form of syndromal X-linked mental retardation called ATR-X syndrome. Mutations or knockdown of ATRX expression cause diverse effects, including altered patterns of DNA methylation, a telomere-dysfunction phenotype, aberrant chromosome segregation, premature sister chromatid separation and changes in gene expression. ATRX localizes predominantly to large, tandemly repeated regions (such as telomeres, centromeres and ribosomal DNA) associated with heterochromatin, and studies show that it directs H3.3 deposition to pericentric and telomeric heterochromatin. The ADD domain of ATRX, in which most syndrome-causing mutations occur, engages the N-terminal tail of histone H3 through two rigidly oriented binding pockets, one for unmodified Lys4 and the other for di- or trimethylated Lys9. Mutations in the ATRX ADD domain cause mislocalization of ATRX protein to heterochromatin, and this may contribute to understanding the underlying etiology of ATRX syndrome. Structure analysis of the ADD domain of ATRX revealed that it contains a PHD zinc-finger domain packed against a GATA-like zinc finger. Same structure is also found in the DNMT3 DNA methyltransferases and DNMT3L [1, 2, 3].	Domain
B [auth C], D [auth F]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D]	Transcriptional regulator ATRX	protein binding binding histone binding chromo shadow domain binding protein domain specific binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding protein binding binding histone binding chromo shadow domain binding protein domain specific binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding methylated histone binding modification-dependent protein binding methylation-dependent protein binding cation binding metal ion binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein-containing complex binding chromatin binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA DNA binding nucleic acid binding chromatin DNA binding DNA translocase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	developmental process multicellular organismal process limb development appendage development post-embryonic appendage morphogenesis forelimb morphogenesis multicellular organism development anatomical structure morphogenesis post-embryonic limb morphogenesis appendage morphogenesis anatomical structure development post-embryonic animal morphogenesis post-embryonic forelimb morphogenesis post-embryonic development developmental process multicellular organismal process limb development appendage development post-embryonic appendage morphogenesis forelimb morphogenesis multicellular organism development anatomical structure morphogenesis post-embryonic limb morphogenesis appendage morphogenesis anatomical structure development post-embryonic animal morphogenesis post-embryonic forelimb morphogenesis post-embryonic development limb morphogenesis spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process replication fork processing regulation of maintenance of mitotic sister chromatid cohesion mitotic sister chromatid cohesion, telomeric negative regulation of maintenance of sister chromatid cohesion regulation of cellular component organization regulation of cellular process negative regulation of maintenance of mitotic sister chromatid cohesion mitotic sister chromatid cohesion regulation of maintenance of mitotic sister chromatid cohesion, telomeric negative regulation of biological process negative regulation of cell cycle maintenance of sister chromatid cohesion maintenance of mitotic sister chromatid cohesion, telomeric cellular component organization negative regulation of sister chromatid cohesion negative regulation of chromosome organization maintenance of mitotic sister chromatid cohesion negative regulation of cellular process cellular component organization or biogenesis cell cycle regulation of cell cycle cell cycle process regulation of biological process negative regulation of cellular component organization regulation of cell cycle process biological regulation chromosome organization sister chromatid cohesion regulation of chromosome organization negative regulation of cell cycle process regulation of organelle organization negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric regulation of maintenance of sister chromatid cohesion organelle organization negative regulation of organelle organization regulation of sister chromatid cohesion cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process microtubule cytoskeleton organization meiotic cell cycle meiotic spindle organization meiotic cell cycle process microtubule-based process cytoskeleton organization spindle organization subtelomeric heterochromatin formation telomere organization negative regulation of cellular metabolic process protein-DNA complex organization chromatin organization chromatin remodeling negative regulation of macromolecule metabolic process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair protein localization localization cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to chromosome, telomeric region positive regulation of organelle organization regulation of telomere maintenance positive regulation of cellular component organization positive regulation of biological process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of telomere maintenance positive regulation of nucleobase-containing compound metabolic process positive regulation of chromosome organization telomere maintenance positive regulation of DNA metabolic process regulation of DNA metabolic process cellular developmental process sex differentiation cell development epithelial cell differentiation Sertoli cell differentiation male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics cell differentiation reproductive structure development system development epithelium development gonad development reproductive system development Sertoli cell development animal organ development tissue development epithelial cell development multicellular organism growth developmental growth growth positive regulation of macromolecule biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process tube development seminiferous tubule development chromosome organization involved in meiotic cell cycle protein-DNA complex assembly cellular component biogenesis cellular component assembly protein-containing complex assembly nucleosome assembly nucleosome organization positive regulation of DNA replication nuclear DNA replication cell cycle DNA replication positive regulation of nuclear cell cycle DNA replication positive regulation of cell cycle process regulation of nuclear cell cycle DNA replication positive regulation of cell cycle regulation of DNA-templated DNA replication positive regulation of DNA-templated DNA replication regulation of DNA replication head development forebrain development brain development nervous system development central nervous system development signaling signal transduction by p53 class mediator DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication signal transduction in response to DNA damage signal transduction cellular response to nitrogen compound cellular response to inorganic substance response to organic substance response to nitrogen compound response to inorganic substance cellular response to hydroxyurea cellular response to chemical stimulus response to hydroxyurea response to chemical	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex protein-DNA complex chromatin heterochromatin chromosome, telomeric region chromosomal region nucleoplasm chromosome, subtelomeric region pericentric heterochromatin chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome nuclear body PML body
B [auth C], D [auth F]	peptide of 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A, C [auth D]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C [auth D]	IPR001650	Helicase, C-terminal domain-like	Domain
A, C [auth D]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C [auth D]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, C [auth D]	IPR041430	ATRX, ADD domain	Domain
A, C [auth D]	IPR025766	ADD domain	Domain
A, C [auth D]	IPR000330	SNF2, N-terminal	Domain
A, C [auth D]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, C [auth D]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
B [auth C], D [auth F]	IPR009072	Histone-fold	Homologous Superfamily
B [auth C], D [auth F]	IPR007125	Histone H2A/H2B/H3	Domain
B [auth C], D [auth F]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth D]	Pharos: P46100	alpha thalassemia-X-linked intellectual disability syndrome alpha-thalassemia-myelodysplastic syndrome intellectual disability malignant glioma myelodysplastic syndrome neuroblastoma glioblastoma mixed glioma neuroendocrine neoplasm Craniofacial Abnormalities salivary gland adenoid cystic carcinoma thoracic disease X-linked intellectual disability-hypotonic face syndrome adenoid cystic carcinoma autism, susceptibility to, X-linked 2 alpha thalassemia-X-linked intellectual disability syndrome alpha-thalassemia-myelodysplastic syndrome intellectual disability malignant glioma myelodysplastic syndrome neuroblastoma glioblastoma mixed glioma neuroendocrine neoplasm Craniofacial Abnormalities salivary gland adenoid cystic carcinoma thoracic disease X-linked intellectual disability-hypotonic face syndrome adenoid cystic carcinoma autism, susceptibility to, X-linked 2 cryptorchidism penile disease psoriasis Smith-Fineman-Myers syndrome ulcerative colitis lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm astrocytic tumor congenital anemia pancreatic endocrine carcinoma Pick disease glioma rheumatoid arthritis hereditary spastic paraplegia spinal cord disease Juberg-Marsidi syndrome lung cancer acute myeloid leukemia medulloblastoma atypical teratoid rhabdoid tumor brain disease osteogenesis imperfecta diabetes mellitus pancreatic neoplasm genetic endocrine growth disease large cell medulloblastoma lymphoplasmacytic lymphoma arthrogryposis microcephaly cancer ovarian cancer
B [auth C], 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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth C], D [auth F]	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.