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Yorodumi- PDB-6gnx: Crystal structure of the MAJIN-TERB2 heterotetrameric complex - s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gnx | |||||||||
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Title | Crystal structure of the MAJIN-TERB2 heterotetrameric complex - selenomethionine derivative | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Meiosis / telomeres / complex | |||||||||
Function / homology | Function and homology information meiotic attachment of telomere to nuclear envelope / meiotic telomere clustering / synaptonemal complex assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / nuclear inner membrane / oogenesis / spermatogenesis / chromosome, telomeric region / DNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | |||||||||
Authors | Gurusaran, M. / Dunce, J.M. / Sen, L.T. / Davies, O.R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis of meiotic telomere attachment to the nuclear envelope by MAJIN-TERB2-TERB1. Authors: Dunce, J.M. / Milburn, A.E. / Gurusaran, M. / da Cruz, I. / Sen, L.T. / Benavente, R. / Davies, O.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gnx.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gnx.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/6gnx ftp://data.pdbj.org/pub/pdb/validation_reports/gn/6gnx | HTTPS FTP |
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-Related structure data
Related structure data | 6gnyC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m36gnx / 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: 13710.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAJIN, C11orf85 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KP22 #2: Protein | Mass: 6371.796 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TERB2, C15orf43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NHR7 |
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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: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol, 55.5 mM MES pH 3.11, 44.5 mM imidazole pH 10.23; 12.5% ...Details: 0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol, 55.5 mM MES pH 3.11, 44.5 mM imidazole pH 10.23; 12.5% w/v PEG 1000; 12.5% w/v PEG 3350; 12.5% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.33 Å / Num. obs: 7915 / % possible obs: 100 % / Redundancy: 56.6 % / CC1/2: 1 / Rpim(I) all: 0.024 / Rrim(I) all: 0.136 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 55.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1250 / CC1/2: 0.885 / Rpim(I) all: 0.553 / Rrim(I) all: 3.015 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→49.329 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 33.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.329 Å
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Refine LS restraints |
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LS refinement shell |
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