1PD0 | pdb_00001pd0

Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide from the SNARE protein Sed5 (yeast syntaxin-5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.254 (Depositor) 
  • R-Value Work: 
    0.206 (Depositor) 
  • R-Value Observed: 
    0.206 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1PD0

This is version 1.3 of the entry. See complete history

Literature

SNARE selectivity of the COPII coat.

Mossessova, E.Bickford, L.C.Goldberg, J.

(2003) Cell 114: 483-495

  • DOI: https://doi.org/10.1016/s0092-8674(03)00608-1
  • Primary Citation Related Structures: 
    1PCX, 1PD0, 1PD1

  • PubMed Abstract: 

    The COPII coat buds transport vesicles from the endoplasmic reticulum that incorporate cargo and SNARE molecules. Here, we show that recognition of the ER-Golgi SNAREs Bet1, Sed5, and Sec22 occurs through three binding sites on the Sec23/24 subcomplex of yeast COPII. The A site binds to the YNNSNPF motif of Sed5. The B site binds to Lxx-L/M-E sequences present in both the Bet1 and Sed5 molecules, as well as to the DxE cargo-sorting signal. A third, spatially distinct site binds to Sec22. COPII selects the free v-SNARE form of Bet1 because the LxxLE sequence is sequestered in the four-helix bundle of the v-/t-SNARE complex. COPII favors Sed5 within the Sed5/Bos1/Sec22 t-SNARE complex because t-SNARE assembly removes autoinhibitory contacts to expose the YNNSNPF motif. The COPII coat seems to be a specific conductor of the fusogenic forms of these SNAREs, suggesting how vesicle fusion specificity may be programmed during budding.


  • Organizational Affiliation
    • Howard Hughes Medical Institute and the Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 92.1 kDa 
  • Atom Count: 6,063 
  • Modeled Residue Count: 744 
  • Deposited Residue Count: 820 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein transport protein Sec24810Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40482 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40482 
Go to UniProtKB:  P40482
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40482
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
COPII-binding peptide of the integral membrane protein SED510N/AMutation(s): 0 
UniProt
Find proteins for Q01590 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01590 
Go to UniProtKB:  Q01590
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01590
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.254 (Depositor) 
  • R-Value Work:  0.206 (Depositor) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.527α = 90
b = 94.527β = 90
c = 197.935γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-19
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations