+Open data
-Basic information
Entry | Database: PDB / ID: 5yk7 | ||||||
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Title | Crystal Structure of Mdm12-Mmm1 complex | ||||||
Components |
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Keywords | LIPID TRANSPORT / Mmm1 / Mdm12 / ERMES / Phospholipid / Membrane contact site | ||||||
Function / homology | Function and homology information ERMES complex / outer mitochondrial membrane protein complex / mitochondrion inheritance / mitochondrial outer membrane translocase complex assembly / lipid transfer activity / aminophospholipid transport / peroxisome organization / mitochondria-associated endoplasmic reticulum membrane contact site / mitochondrial genome maintenance / phospholipid homeostasis ...ERMES complex / outer mitochondrial membrane protein complex / mitochondrion inheritance / mitochondrial outer membrane translocase complex assembly / lipid transfer activity / aminophospholipid transport / peroxisome organization / mitochondria-associated endoplasmic reticulum membrane contact site / mitochondrial genome maintenance / phospholipid homeostasis / phospholipid transport / lipid transport / protein insertion into mitochondrial outer membrane / mitochondrion-endoplasmic reticulum membrane tethering / mitochondrion organization / mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane / mitochondrion / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Zygosaccharomyces rouxii (yeast) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.799 Å | ||||||
Authors | Jeong, H. / Park, J. / Lee, C. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Crystal structures of Mmm1 and Mdm12-Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites. Authors: Jeong, H. / Park, J. / Jun, Y. / Lee, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yk7.cif.gz | 368.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yk7.ent.gz | 305.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5yk7 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5yk7 | HTTPS FTP |
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-Related structure data
Related structure data | 5yk6C 5gydS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29583.342 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zygosaccharomyces rouxii (strain ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229) (yeast) Strain: ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229 Gene: MMM1, ZYRO0B10274g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5DRQ1 #2: Protein | Mass: 23487.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MDM12, YOL009C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92328 #3: Chemical | ChemComp-PO4 / |
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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: 4.73 Å3/Da / Density % sol: 74.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, HEPES, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 18459 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 3.8→3.87 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GYD Resolution: 3.799→39.142 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.799→39.142 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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