+Open data
-Basic information
Entry | Database: PDB / ID: 3mv3 | ||||||
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Title | Crystal Structure of a-COP in Complex with e-COP | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Vesicular Membrane Coat Coat Protein Complex I | ||||||
Function / homology | Function and homology information vesicle coating / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / intracellular mRNA localization / late endosome to vacuole transport via multivesicular body sorting pathway / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding ...vesicle coating / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / intracellular mRNA localization / late endosome to vacuole transport via multivesicular body sorting pathway / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / promoter-specific chromatin binding / intracellular protein transport / protein transport / Golgi membrane / structural molecule activity Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å | ||||||
Authors | Hoelz, A. / Hsia, K.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Crystal structure of alpha-COP in complex with epsilon-COP provides insight into the architecture of the COPI vesicular coat. Authors: Hsia, K.C. / Hoelz, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mv3.cif.gz | 324.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mv3.ent.gz | 276.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/3mv3 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/3mv3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 36805.062 Da / Num. of mol.: 3 / Fragment: UNP residues 900-1201 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RET1, COP1, SEC33, YDL145C, D1578 / Production host: Escherichia coli (E. coli) / References: UniProt: P53622 #2: Protein | Mass: 35662.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEC28, YIL076W / Production host: Escherichia coli (E. coli) / References: UniProt: P40509 |
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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: 2.64 Å3/Da / Density % sol: 53.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 100 mM HEPES, pH 7.2 8 % (w/v) tacsimate 100 mM sodium malonate 200 mM sodium chloride 20 % (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9796 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. obs: 62887 / Redundancy: 3.8 % / Rsym value: 0.103 |
Reflection shell | Resolution: 3.25→3.37 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.735 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.25→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 98.764 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 201.88 Å2 / Biso mean: 128.721 Å2 / Biso min: 8.23 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→50 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: CNS_TOPPAR:protein_rep.param |