2PM9

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.251 

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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: 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein SEC31A416Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: WEB1, SEC31
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein SEC13B297Saccharomyces cerevisiaeMutation(s): 6 
Gene Names: SEC13, ANU3
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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.251 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.163α = 90
b = 155.163β = 90
c = 59.866γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

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: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references