+Open data
-Basic information
Entry | Database: PDB / ID: 6gny | |||||||||
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Title | Crystal structure of the MAJIN-TERB2 heterotetrameric complex | |||||||||
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 / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / nuclear inner membrane / oogenesis / spermatogenesis / chromosome, telomeric region / DNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Dunce, J.M. / Gurusaran, 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 | 6gny.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gny.ent.gz | 148 KB | Display | PDB format |
PDBx/mmJSON format | 6gny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gny_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 6gny_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 6gny_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6gny_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/6gny ftp://data.pdbj.org/pub/pdb/validation_reports/gn/6gny | HTTPS FTP |
-Related structure data
Related structure data | 6gnxSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m36gny / 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: 12755.706 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/peptide | Mass: 4750.389 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 #3: Chemical | ChemComp-TRS / | #4: 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: 2.11 Å3/Da / Density % sol: 41.8 % |
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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; 39.1 mM bicine pH 5.03; 60.9 mM Trizma pH 10.83; 18.3% ...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; 39.1 mM bicine pH 5.03; 60.9 mM Trizma pH 10.83; 18.3% w/v PEG 1000; 18.3% w/v PEG 3350; 18.3% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→45.35 Å / Num. obs: 25741 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 44.57 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.014 / Rrim(I) all: 0.039 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1565 / CC1/2: 0.744 / Rpim(I) all: 0.504 / Rrim(I) all: 1.374 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GNX Resolution: 1.85→45.35 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 26.01
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→45.35 Å
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Refine LS restraints |
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LS refinement shell |
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