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Yorodumi- PDB-7uva: Crystal structure of KDM2A histone demethylase catalytic domain i... -
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-Basic information
Entry | Database: PDB / ID: 7uva | ||||||||||||||||||
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Title | Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 | ||||||||||||||||||
Components |
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Keywords | GENE REGULATION / demethylase / histone / inhibitor | ||||||||||||||||||
Function / homology | Function and homology information histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / HDMs demethylate histones / neuroepithelial cell differentiation / unmethylated CpG binding / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / histone demethylase activity / Chromatin modifying enzymes ...histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / HDMs demethylate histones / neuroepithelial cell differentiation / unmethylated CpG binding / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / histone demethylase activity / Chromatin modifying enzymes / transcription initiation-coupled chromatin remodeling / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / neural tube closure / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / transcription coregulator activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / circadian regulation of gene expression / multicellular organism growth / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / regulation of circadian rhythm / neuron differentiation / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / double-strand break repair via nonhomologous end joining / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / in utero embryonic development / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||||||||||||||
Authors | Budziszewski, G.R. / Azzam, D.N. / Spangler, C.J. / Skrajna, A. / Foley, C.A. / James, L.I. / Frye, S.V. / McGinty, R.K. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Nat Chem Biol / Year: 2023 Title: Structural basis of paralog-specific KDM2A/B nucleosome recognition. Authors: Cathy J Spangler / Aleksandra Skrajna / Caroline A Foley / Anh Nguyen / Gabrielle R Budziszewski / Dalal N Azzam / Eyla C Arteaga / Holly C Simmons / Charlotte B Smith / Nathaniel A Wesley / ...Authors: Cathy J Spangler / Aleksandra Skrajna / Caroline A Foley / Anh Nguyen / Gabrielle R Budziszewski / Dalal N Azzam / Eyla C Arteaga / Holly C Simmons / Charlotte B Smith / Nathaniel A Wesley / Emily M Wilkerson / Jeanne-Marie E McPherson / Dmitri Kireev / Lindsey I James / Stephen V Frye / Dennis Goldfarb / Robert K McGinty / Abstract: The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. To define the molecular basis of acidic ...The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. To define the molecular basis of acidic patch recognition proteome wide, we performed an amino acid resolution acidic patch interactome screen. We discovered that the histone H3 lysine 36 (H3K36) demethylase KDM2A, but not its closely related paralog, KDM2B, requires the acidic patch for nucleosome binding. Despite fundamental roles in transcriptional repression in health and disease, the molecular mechanisms governing nucleosome substrate specificity of KDM2A/B, or any related JumonjiC (JmjC) domain lysine demethylase, remain unclear. We used a covalent conjugate between H3K36 and a demethylase inhibitor to solve cryogenic electron microscopy structures of KDM2A and KDM2B trapped in action on a nucleosome substrate. Our structures show that KDM2-nucleosome binding is paralog specific and facilitated by dynamic nucleosomal DNA unwrapping and histone charge shielding that mobilize the H3K36 sequence for demethylation. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uva.cif.gz | 190 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uva.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 7uva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/7uva ftp://data.pdbj.org/pub/pdb/validation_reports/uv/7uva | HTTPS FTP |
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-Related structure data
Related structure data | 7uv9C 4qx7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Lysine-specific demethylase ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 39162.516 Da / Num. of mol.: 2 / Fragment: UNP residues 36-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbl11, Fbxl11, Jhdm1a, Kiaa1004 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS References: UniProt: P59997, [histone H3]-dimethyl-L-lysine36 demethylase #2: Protein | Mass: 7665.956 Da / Num. of mol.: 2 / Fragment: UNP residues 450-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbl11, Fbxl11, Jhdm1a, Kiaa1004 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS References: UniProt: P59997, [histone H3]-dimethyl-L-lysine36 demethylase |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 1359.576 Da / Num. of mol.: 2 / Fragment: UNP residues 30-42 / Mutation: K36C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3 |
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-Non-polymers , 3 types, 433 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→88.09 Å / Num. obs: 58130 / % possible obs: 97.35 % / Redundancy: 6.3 % / Biso Wilson estimate: 36.82 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.09 / Rrim(I) all: 0.22 / Net I/σ(I): 6.48 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 6.7 % / Num. unique obs: 4103 / CC1/2: 0.674 / % possible all: 98.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4QX7 Resolution: 1.98→88.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.623 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.473 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→88.09 Å
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