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- PDB-2j3r: The crystal structure of the bet3-trs31 heterodimer. -

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Basic information

Entry
Database: PDB / ID: 2j3r
TitleThe crystal structure of the bet3-trs31 heterodimer.
Components
  • TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
  • ZGC 92866
KeywordsTRANSPORT / GOLGI APPARATUS / VESICLE TRANSPORT / ER-GOLGI TRANSPORT / TRAPP / PALMITATE / LIPOPROTEIN / ENDOPLASMIC RETICULUM / MULTISUBUNIT TETHERING FACTOR
Function / homology
Function and homology information


COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / vesicle coating / vesicle tethering / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / COPII-mediated vesicle transport / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex ...COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / vesicle coating / vesicle tethering / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / COPII-mediated vesicle transport / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / intra-Golgi vesicle-mediated transport / cis-Golgi network membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / Golgi membrane / Golgi apparatus / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Trafficking protein particle complex subunit 3 / TRAPP I complex, subunit 5 / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / PALMITIC ACID / Trafficking protein particle complex subunit 3 / Trafficking protein particle complex subunit 5
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
BRACHYDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKim, Y.-G. / Oh, B.-H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: The Architecture of the Multisubunit Trapp I Complex Suggests a Model for Vesicle Tethering.
Authors: Kim, Y.-G. / Raunser, S. / Munger, C. / Wagner, J. / Song, Y.-L. / Cygler, M. / Walz, T. / Oh, B.-H. / Sacher, M.
History
DepositionAug 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
B: ZGC 92866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3074
Polymers37,9882
Non-polymers3182
Water55831
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-22.9 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.492, 93.348, 60.988
Angle α, β, γ (deg.)90.00, 92.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3 / BET3 HOMOLOG


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
#2: Protein ZGC 92866 / TRS31


Mass: 17536.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRACHYDANIO RERIO (zebrafish) / Plasmid: PPROEXHTA, PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DGL5
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.13 %
Crystal growpH: 8
Details: 0.26 M AMMONIUM NITRATE AND 14% (W/V) POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, pH 8.00

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→30 Å / Num. obs: 14269 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 53.2
Reflection shellHighest resolution: 2.56 Å / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 10.5 / % possible all: 78.5

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→30 Å / Data cutoff high absF: 10000 / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 712 4.9 %RANDOM
Rwork0.22 ---
obs0.22 14269 98.9 %-
Solvent computationBsol: 32.4956 Å2 / ksol: 0.310941 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--26.873 Å20 Å23.83 Å2
2--11.926 Å20 Å2
3---14.946 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 21 31 2484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2252
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2PLM.PAR
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4NO3.PAR

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