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Yorodumi- PDB-3cue: Crystal structure of a TRAPP subassembly activating the Rab Ypt1p -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cue | ||||||
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Title | Crystal structure of a TRAPP subassembly activating the Rab Ypt1p | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / membrane traffic / GEF / tethering complex / Rab activation / guanine nucleotide exchange factor / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Transport / Lipoprotein / Palmitate / GTP-binding / Nucleotide-binding / Phosphoprotein / Prenylation | ||||||
Function / homology | Function and homology information pre-mRNA catabolic process / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / TRAPPI protein complex / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex ...pre-mRNA catabolic process / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / TRAPPI protein complex / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-coated vesicle budding / COPII-mediated vesicle transport / cytoplasm to vacuole targeting by the Cvt pathway / intra-Golgi vesicle-mediated transport / protein localization to phagophore assembly site / phagophore assembly site membrane / Golgi stack / cis-Golgi network / endocytic recycling / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / reticulophagy / retrograde transport, endosome to Golgi / cis-Golgi network membrane / SNARE complex assembly / autophagosome assembly / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / Neutrophil degranulation / SNARE binding / macroautophagy / intracellular protein transport / cytoplasmic vesicle / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.7 Å | ||||||
Authors | Cai, Y. / Reinisch, K.M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 Title: The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes. Authors: Cai, Y. / Chin, H.F. / Lazarova, D. / Menon, S. / Fu, C. / Cai, H. / Sclafani, A. / Rodgers, D.W. / De La Cruz, E.M. / Ferro-Novick, S. / Reinisch, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cue.cif.gz | 818.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cue.ent.gz | 676.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/3cue ftp://data.pdbj.org/pub/pdb/validation_reports/cu/3cue | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Transport protein particle ... , 4 types, 20 molecules AGMSBHNTCIOUDEJKPQVW
#1: Protein | Mass: 24889.262 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TRS23 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q03784 #2: Protein | Mass: 31755.689 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TRS31 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q03337 #3: Protein | Mass: 18453.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BET5 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q03630 #4: Protein | Mass: 22152.445 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BET3 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P36149 |
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-Protein / Non-polymers , 2 types, 8 molecules FLRX
#5: Protein | Mass: 23240.227 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YPT1, YP2 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P01123 #6: Chemical | ChemComp-PLM / |
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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: 3.38 Å3/Da / Density % sol: 63.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 3-5% PEG 20,000, 0.1 M MES, 3% (w/v) sorbitol, 5 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795, 0.9537 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2007 | |||||||||
Radiation | Monochromator: single crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.7→50 Å / Num. all: 81195 / Num. obs: 81195 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 11.6 | |||||||||
Reflection shell | Resolution: 3.7→3.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7251 / Rsym value: 0.368 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.7→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.7→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.7→3.72 Å /
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