3DIN Membrane Protein, Protein Transport date Jun 20, 2008
title Crystal Structure Of The Protein-Translocation Complex Forme Secy Channel And The Seca Atpase
authors J.Zimmer, Y.Nam, T.A.Rapoport
compound source
Molecule: Protein Translocase Subunit Seca
Chain: A, B
Engineered: Yes
Organism_scientific: Thermotoga Maritima Msb8
Organism_taxid: 243274
Strain: Msb8 Dsm 3109 Jcm 10099
Atcc: 43589
Gene: Seca, Tm_1578
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Preprotein Translocase Subunit Secy
Chain: C, F
Engineered: Yes

Organism_scientific: Thermotoga Maritima Msb8
Organism_taxid: 243274
Strain: Msb8 Dsm 3109 Jcm 10099
Atcc: 43589
Gene: Secy, Tm_1480
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Preprotein Translocase Subunit Sece
Chain: D, G
Engineered: Yes

Organism_scientific: Thermotoga Maritima Msb8
Organism_taxid: 243274
Strain: Msb8 Dsm 3109 Jcm 10099
Atcc: 43589
Gene: Sece, Tm_0452
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Preprotein Translocase Subunit Secg
Chain: E, H
Engineered: Yes

Organism_scientific: Thermotoga Sp.
Organism_taxid: 126740
Strain: Rq2
Gene: Secg, Trq2_0456
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.279 R_Free 0.303
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.616 156.003 358.155 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.50 Å
ligand ADP, BEF, MG enzyme
Gene TM ; TM ; TM ; TRQ2
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, G


E, H
  • P-P-bond-hydrolysis-driven p...


  • F, C


    Primary referenceStructure of a complex of the ATPase SecA and the protein-translocation channel., Zimmer J, Nam Y, Rapoport TA, Nature. 2008 Oct 16;455(7215):936-43. PMID:18923516
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (403 Kb) [Save to disk]
  • Biological Unit Coordinates (3din.pdb1.gz) 202 Kb
  • Biological Unit Coordinates (3din.pdb2.gz) 200 Kb
  • LPC: Ligand-Protein Contacts for 3DIN
  • CSU: Contacts of Structural Units for 3DIN
  • Likely Quarternary Molecular Structure file(s) for 3DIN
  • Structure Factors (620 Kb)
  • Retrieve 3DIN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DIN from S2C, [Save to disk]
  • Re-refined 3din structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DIN in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3DIN
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3DIN, from MSDmotif at EBI
  • Fold representative 3din from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3din_G] [3din_E] [3din_] [3din_A] [3din_B] [3din_H] [3din_C] [3din_D] [3din_F] [3din]
  • SWISS-PROT database: [B1L914] [Q9X1I9] [Q9X1R4] [P35874]
  • Domain organization of [B1L914_THESQ] [Q9X1I9_THEMA] [SECA_THEMA] [SECE_THEMA] by SWISSPFAM
  • Domains found in 3DIN: [SecA_DEAD] [SecA_PP_bind ] by SMART
  • Other resources with information on 3DIN
  • Community annotation for 3DIN at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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