1MM2 | pdb_00001mm2

Solution structure of the 2nd PHD domain from Mi2b

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1mm2a1	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	PHD domain	Mi2-beta (CHD4)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1mm2a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PHD domain	8020412	4003778	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FYVE/PHD zinc finger	8032792	3001459	SCOP2 (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	PHD_1	e1mm2A1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Mi2-beta	ATP-dependent activity, acting on DNA catalytic activity, acting on DNA DNA translocase activity catalytic activity, acting on a nucleic acid chromatin extrusion motor activity catalytic activity ATP-dependent activity ATP-dependent H3-H4 histone complex chaperone activity catalytic activity, acting on a protein histone chaperone activity ATP-dependent chromatin remodeler activity H3-H4 histone complex chaperone activity protein carrier chaperone ATP-dependent histone chaperone activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA DNA translocase activity catalytic activity, acting on a nucleic acid chromatin extrusion motor activity catalytic activity ATP-dependent activity ATP-dependent H3-H4 histone complex chaperone activity catalytic activity, acting on a protein histone chaperone activity ATP-dependent chromatin remodeler activity H3-H4 histone complex chaperone activity protein carrier chaperone ATP-dependent histone chaperone activity molecular carrier activity protein binding binding histone binding histone deacetylase binding enzyme binding nucleic acid conformation isomerase activity forked DNA-dependent helicase activity isomerase activity DNA helicase activity helicase activity macromolecular conformation isomerase activity transcription factor binding transcription coregulator binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding double-stranded DNA helicase activity cohesin loader activity DNA clamp loader activity RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromatin binding ATP-dependent H2AZ histone chaperone activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity single-stranded DNA helicase activity 3'-5' DNA helicase activity single-stranded 3'-5' DNA helicase activity four-way junction helicase 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 cation binding transition metal ion binding zinc ion binding metal ion binding	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process multicellular organismal process regulation of cellular component organization cellular component organization developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process multicellular organismal process regulation of cellular component organization cellular component organization cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly anatomical structure development regulation of synapse structure or activity regulation of synapse assembly synapse organization cellular component organization or biogenesis regulation of biological quality system development nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process 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 regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process presynapse organization terminal button organization regulation of cell fate commitment cell fate specification regulation of cell fate specification cell fate commitment cellular response to stimulus double-strand break repair response to stimulus DNA recombination DNA metabolic process cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair 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 nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process negative regulation of gene expression chromatin organization chromatin remodeling	cellular anatomical structure membrane neuron to neuron synapse synapse cell junction asymmetric synapse cerebellar granule cell to Purkinje cell synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse intracellular anatomical structure cytoplasm intracellular organelle organelle cellular anatomical structure membrane neuron to neuron synapse synapse cell junction asymmetric synapse cerebellar granule cell to Purkinje cell synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle protein-containing complex ATPase complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular organelle lumen histone deacetylase complex nucleoplasm NuRD complex SWI/SNF superfamily-type complex catalytic complex intracellular membrane-bounded organelle organelle lumen CHD-type complex nuclear lumen chromosome, telomeric region chromosomal region RNA polymerase II transcription regulator complex centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR012958	CHD, N-terminal	Domain
A	IPR012957	CHD, C-terminal 2	Domain
A	IPR000330	SNF2, N-terminal	Domain
A	IPR023780	Chromo domain	Domain
A	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR002464	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	Conserved Site
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A	IPR000953	Chromo/chromo shadow domain	Domain
A	IPR009462	CHD subfamily II, SANT-like domain	Domain
A	IPR009463	Domain of unknown function DUF1087	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q14839	Sifrim-Hitz-Weiss syndrome endometrial carcinoma intellectual disability schizophrenia astrocytic tumor endometrial cancer glioblastoma lung adenocarcinoma osteosarcoma psoriasis autism malignant mesothelioma ovarian cancer rheumatoid arthritis developmental disability Sifrim-Hitz-Weiss syndrome endometrial carcinoma intellectual disability schizophrenia astrocytic tumor endometrial cancer glioblastoma lung adenocarcinoma osteosarcoma psoriasis autism malignant mesothelioma ovarian cancer rheumatoid arthritis developmental disability Endometrial Neoplasms large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor

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.