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Yorodumi- PDB-2duo: Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+-bound form -
+Open data
-Basic information
Entry | Database: PDB / ID: 2duo | ||||||
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Title | Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+-bound form | ||||||
Components | Vesicular integral-membrane protein VIP36 | ||||||
Keywords | PROTEIN TRANSPORT / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN / CARGO RECEPTOR | ||||||
Function / homology | Function and homology information COPII-mediated vesicle transport / Cargo concentration in the ER / COPI-coated vesicle / exocytic vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-coated ER to Golgi transport vesicle / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of phagocytosis ...COPII-mediated vesicle transport / Cargo concentration in the ER / COPI-coated vesicle / exocytic vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-coated ER to Golgi transport vesicle / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of phagocytosis / heat shock protein binding / protein transport / cytoplasmic vesicle / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / extracellular space / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Satoh, T. / Cowieson, N.P. / Kato, R. / Wakatsuki, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36 Authors: Satoh, T. / Cowieson, N.P. / Hakamata, W. / Ideo, H. / Fukushima, K. / Kurihara, M. / Kato, R. / Yamashita, K. / Wakatsuki, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2duo.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2duo.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 2duo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/2duo ftp://data.pdbj.org/pub/pdb/validation_reports/du/2duo | HTTPS FTP |
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-Related structure data
Related structure data | 2dupC 2duqC 2durC 2e6vC 1r1zS 2dus 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28931.318 Da / Num. of mol.: 2 / Fragment: RESIDUES 51-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: LMAN2 / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49256 #2: Chemical | #3: Chemical | ChemComp-CL / #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: 2.91 Å3/Da / Density % sol: 57.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG4000, 1.5M NaCl, 0.1M MES (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 62420 / Num. obs: 61028 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5986 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R1Z Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.773 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.8 Å / Num. reflection Rwork: 4173 / Total num. of bins used: 20 |