+Open data
-Basic information
Entry | Database: PDB / ID: 2j3t | ||||||
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Title | The crystal structure of the bet3-trs33-bet5-trs23 complex. | ||||||
Components | (TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT ...) x 4 | ||||||
Keywords | TRANSPORT / TRAPP / PALMITATE / LIPOPROTEIN / ER-GOLGI TRANSPORT / GOLGI APPARATUS / PROTEIN TRANSPORT / VESICLE TRANSPORT / ENDOPLASMIC RETICULUM / MULTISUBUNIT TETHERING FACTOR | ||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor activity => GO:0005085 / vesicle coating / vesicle tethering / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / cis-Golgi network membrane / COPII vesicle coating ...guanyl-nucleotide exchange factor activity => GO:0005085 / vesicle coating / vesicle tethering / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / cis-Golgi network membrane / COPII vesicle coating / intra-Golgi vesicle-mediated transport / Golgi stack / RAB GEFs exchange GTP for GDP on RABs / cis-Golgi network / COPII-mediated vesicle transport / Syndecan interactions / dendrite development / endoplasmic reticulum to Golgi vesicle-mediated transport / Neutrophil degranulation / trans-Golgi network / autophagy / synaptic vesicle / postsynaptic membrane / Golgi membrane / synapse / dendrite / Golgi apparatus / endoplasmic reticulum / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Kim, Y. / Oh, B. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: The Architecture of the Multisubunit Trapp I Complex Suggests a Model for Vesicle Tethering. Authors: Kim, Y. / Raunser, S. / Munger, C. / Wagner, J. / Song, Y. / Cygler, M. / Walz, T. / Oh, B. / Sacher, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j3t.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j3t.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 2j3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j3t_validation.pdf.gz | 593.8 KB | Display | wwPDB validaton report |
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Full document | 2j3t_full_validation.pdf.gz | 612.8 KB | Display | |
Data in XML | 2j3t_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 2j3t_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/2j3t ftp://data.pdbj.org/pub/pdb/validation_reports/j3/2j3t | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 20452.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPROEXHTA, PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O55013 |
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#2: Protein | Mass: 17620.486 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTA, PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75865 |
#3: Protein | Mass: 16905.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPROEXHTA, PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NCF2 |
#4: Protein | Mass: 24365.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTA, PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y296 |
-Non-polymers , 2 types, 133 molecules
#5: Chemical | ChemComp-PLM / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 8.5 Details: 20% (W/V) PEG 3350, 0.28 M LITHIUM SULFATE AND 0.1 M TRIS HCL (PH 8.5) |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 25464 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.2 |
Reflection shell | Highest resolution: 2.4 Å / Mean I/σ(I) obs: 5.9 / % possible all: 78.9 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.4→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 18.8036 Å2 / ksol: 0.313366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Xplor file |
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