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Yorodumi- PDB-1z9l: 1.7 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z9l | ||||||
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Title | 1.7 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain | ||||||
Components | Vesicle-associated membrane protein-associated protein A | ||||||
Keywords | PROTEIN BINDING / VAP-A / Cytoplasmic domain | ||||||
Function / homology | Function and homology information FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / ceramide transport / protein localization to endoplasmic reticulum / sphingomyelin biosynthetic process / sterol transport / positive regulation by host of viral genome replication / COPII-coated vesicle budding / negative regulation by host of viral genome replication / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane ...FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / ceramide transport / protein localization to endoplasmic reticulum / sphingomyelin biosynthetic process / sterol transport / positive regulation by host of viral genome replication / COPII-coated vesicle budding / negative regulation by host of viral genome replication / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / phospholipid transport / cholesterol transport / Neutrophil degranulation / viral release from host cell / bicellular tight junction / endoplasmic reticulum to Golgi vesicle-mediated transport / neuron projection development / microtubule cytoskeleton / microtubule binding / nuclear membrane / vesicle / protein heterodimerization activity / protein domain specific binding / Golgi membrane / protein-containing complex binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Kaiser, S.E. / Brickner, J.H. / Reilein, A.R. / Fenn, T.D. / Walter, P. / Brunger, A.T. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Structural basis of FFAT motif-mediated ER targeting Authors: Kaiser, S.E. / Brickner, J.H. / Reilein, A.R. / Fenn, T.D. / Walter, P. / Brunger, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z9l.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z9l.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 1z9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/1z9l ftp://data.pdbj.org/pub/pdb/validation_reports/z9/1z9l | HTTPS FTP |
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-Related 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: 14827.251 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vapa, Vap33 / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Z270 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG2000 MME, NaCl, tris buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795, 0.9793, 0.9649 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2002 | ||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. all: 27524 / Num. obs: 27860 / % possible obs: 98.8 % / Observed criterion σ(F): 8 / Observed criterion σ(I): 8 / Biso Wilson estimate: 17.4 Å2 | ||||||||||||
Reflection shell | Resolution: 1.7→1.79 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→13.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 824290.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.178 Å2 / ksol: 0.365461 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→13.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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