2PM9

Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.cell.2007.05.036
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein SEC31
A
416Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SEC31 (WEB1)
Find proteins for P38968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38968
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein SEC13
B
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 6 
Gene Names: SEC13 (ANU3)
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SEC13
Go to UniProtKB:  Q04491
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.251 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 155.163α = 90.00
b = 155.163β = 90.00
c = 59.866γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction
CNSrefinement
RESOLVEphasing
SCALEPACKdata scaling
AMoREphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description