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Yorodumi- PDB-5ofa: Crystal structure of human MORC2 (residues 1-603) with spinal mus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ofa | |||||||||
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Title | Crystal structure of human MORC2 (residues 1-603) with spinal muscular atrophy mutation T424R | |||||||||
Components | MORC family CW-type zinc finger protein 2 | |||||||||
Keywords | NUCLEAR PROTEIN / GHKL ATPase / chromatin remodeler / epigenetic silencing / transcriptional repressor / coiled-coil / CW domain / DNA binding protein / Charcot-Marie-Tooth disease / spinal muscular atrophy | |||||||||
Function / homology | Function and homology information positive regulation of DNA methylation-dependent heterochromatin formation / Fatty acyl-CoA biosynthesis / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression, epigenetic / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / heterochromatin / fatty acid metabolic process / nuclear matrix / chromatin remodeling / DNA damage response ...positive regulation of DNA methylation-dependent heterochromatin formation / Fatty acyl-CoA biosynthesis / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression, epigenetic / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / heterochromatin / fatty acid metabolic process / nuclear matrix / chromatin remodeling / DNA damage response / chromatin binding / magnesium ion binding / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | |||||||||
Authors | Douse, C.H. / Liu, Y. / Modis, Y. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Neuropathic MORC2 mutations perturb GHKL ATPase dimerization dynamics and epigenetic silencing by multiple structural mechanisms. Authors: Douse, C.H. / Bloor, S. / Liu, Y. / Shamin, M. / Tchasovnikarova, I.A. / Timms, R.T. / Lehner, P.J. / Modis, Y. #1: Journal: Nat. Genet. / Year: 2017 Title: Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2. Authors: Tchasovnikarova, I.A. / Timms, R.T. / Douse, C.H. / Roberts, R.C. / Dougan, G. / Kingston, R.E. / Modis, Y. / Lehner, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ofa.cif.gz | 448.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ofa.ent.gz | 381.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ofa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/5ofa ftp://data.pdbj.org/pub/pdb/validation_reports/of/5ofa | HTTPS FTP |
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-Related structure data
Related structure data | 5of9C 5ofbC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/476 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 70075.094 Da / Num. of mol.: 2 / Mutation: T424R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MORC2, KIAA0852, ZCWCC1 Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: Q9Y6X9 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48 % / Description: Plates |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M bicine/Trizma pH 8.5 10.8% PEG 4k 21.6% glycerol 0.02 M each of the following: 1,6-hexanediol; 1-butanol; RS-1,2 propanediol; 2-propanol; 1,4-butanediol; 1,3-propanediol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975999 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.975999 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.574→80.755 Å / Num. obs: 43876 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.037 / Net I/σ(I): 16.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Wild-type human MORC2 Resolution: 2.57→80.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 21.863 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.644 / ESU R Free: 0.288 / 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: 91.267 Å2
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Refinement step | Cycle: 1 / Resolution: 2.57→80.75 Å
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