[English] 日本語
Yorodumi
- PDB-2j3w: The crystal structure of the bet3-trs31-sedlin complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j3w
TitleThe crystal structure of the bet3-trs31-sedlin complex.
Components
  • TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2
  • TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
  • ZGC 92866
KeywordsTRANSPORT / MULTISUBUNIT TETHERING FACTOR / TRAPP / PALMITATE / LIPOPROTEIN / ER-GOLGI TRANSPORT / ENDOPLASMIC RETICULUM / TRANSCRIPTION / GOLGI APPARATUS / VESICLE TRANSPORT
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-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / transcription corepressor binding / skeletal system development / transmembrane transporter binding / Golgi membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Beta-Lactamase - #70 / Trafficking protein particle complex subunit 3 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / 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 ...Beta-Lactamase - #70 / Trafficking protein particle complex subunit 3 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / 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 / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Trafficking protein particle complex subunit 3 / Trafficking protein particle complex subunit 5 / Trafficking protein particle complex subunit 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
BRACHYDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Aug 7, 2013Group: Other / Source and taxonomy

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2
B: ZGC 92866
C: TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2
D: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
E: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
F: ZGC 92866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9468
Polymers116,4336
Non-polymers5132
Water3,873215
1
C: TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2
D: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
F: ZGC 92866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4734
Polymers58,2173
Non-polymers2561
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-41.5 kcal/mol
Surface area21370 Å2
MethodPISA
2
A: TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2
B: ZGC 92866
E: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4734
Polymers58,2173
Non-polymers2561
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-38.7 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.211, 63.063, 72.018
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2 / SEDLIN


Mass: 16705.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPROEXHTA, PET15B, PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CQP2
#2: Protein ZGC 92866


Mass: 21059.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRACHYDANIO RERIO (zebrafish) / Plasmid: PPROEXHTA, PET15B, PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DGL5
#3: Protein TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3 / BET3 HOMOLOG


Mass: 20452.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPROEXHTA, PET15B, PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O55013
#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 8
Details: 20% (W/V) PEG3350, 0.2 M MGCL2, 2% (W/V) BENZAMIDINE AND 0.1 M TRIS HCL (PH 8.0)

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / 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: 2.1→30 Å / Num. obs: 57111 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29
Reflection shellHighest resolution: 2.1 Å / Mean I/σ(I) obs: 4.2 / % possible all: 73.4

-
Processing

Software
NameClassification
CNSrefinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 2892 4.7 %RANDOM
Rwork0.2296 ---
obs0.2296 57111 93.6 %-
Solvent computationBsol: 39.3699 Å2 / ksol: 0.347067 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.27 Å20 Å211.263 Å2
2--7.183 Å20 Å2
3----12.454 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7348 0 34 215 7597
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
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_deg1.1519
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more