2PM6

Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native version


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure and Organization of Coat Proteins in the COPII Cage.

Fath, S.Mancias, J.D.Bi, X.Goldberg, J.

(2007) Cell 129: 1325-1336

  • DOI: https://doi.org/10.1016/j.cell.2007.05.036
  • Primary Citation of Related Structures:  
    2PM6, 2PM7, 2PM9

  • PubMed Abstract: 

    COPII-coated vesicles export newly synthesized proteins from the endoplasmic reticulum. The COPII coat consists of the Sec23/24-Sar1 complex that selects cargo and the Sec13/31 assembly unit that can polymerize into an octahedral cage and deform the membrane into a bud. Crystallographic analysis of the assembly unit reveals a 28 nm long rod comprising a central alpha-solenoid dimer capped by two beta-propeller domains at each end. We construct a molecular model of the COPII cage by fitting Sec13/31 crystal structures into a recently determined electron microscopy density map. The vertex geometry involves four copies of the Sec31 beta-propeller that converge through their axial ends; there is no interdigitation of assembly units of the kind seen in clathrin cages. We also propose that the assembly unit has a central hinge-an arrangement of interlocked alpha-solenoids-about which it can bend to adapt to cages of variable curvature.


  • Organizational Affiliation

    Howard Hughes Medical Institute and the Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC31
A, C
399Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: WEB1SEC31
UniProt
Find proteins for P38968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38968 
Go to UniProtKB:  P38968
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38968
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC13
B, D
297Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEC13ANU3
UniProt
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04491 
Go to UniProtKB:  Q04491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04491
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.387α = 90
b = 52.343β = 108.62
c = 133.128γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references
  • Version 1.4: 2024-04-03
    Changes: Refinement description