3EFO

Crystal Structure of the mammalian COPII-coat protein Sec23/24 bound to the transport signal sequence of syntaxin 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of cargo membrane protein discrimination by the human COPII coat machinery.

Mancias, J.D.Goldberg, J.

(2008) EMBO J 27: 2918-2928

  • DOI: https://doi.org/10.1038/emboj.2008.208
  • Primary Citation of Related Structures:  
    3EFO, 3EG9, 3EGD, 3EGX, 3EH1, 3EH2

  • PubMed Abstract: 

    Genomic analysis shows that the increased complexity of trafficking pathways in mammalian cells involves an expansion of the number of SNARE, Rab and COP proteins. Thus, the human genome encodes four forms of Sec24, the cargo selection subunit of the COPII vesicular coat, and this is proposed to increase the range of cargo accommodated by human COPII-coated vesicles. In this study, we combined X-ray crystallographic and biochemical analysis with functional assays of cargo packaging into COPII vesicles to establish molecular mechanisms for cargo discrimination by human Sec24 subunits. A conserved IxM packaging signal binds in a surface groove of Sec24c and Sec24d, but the groove is occluded in the Sec24a and Sec24b subunits. Conversely, LxxLE class transport signals and the DxE signal of VSV glycoprotein are selectively bound by Sec24a and Sec24b subunits. A comparative analysis of crystal structures of the four human Sec24 isoforms establishes the structural determinants for discrimination among these transport signals, and provides a framework to understand how an expansion of coat subunits extends the range of cargo proteins packaged into COPII-coated vesicles.


  • Organizational Affiliation

    Howard Hughes Medical Institute and the Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec23A765Homo sapiensMutation(s): 0 
Gene Names: SEC23A
UniProt & NIH Common Fund Data Resources
Find proteins for Q15436 (Homo sapiens)
Explore Q15436 
Go to UniProtKB:  Q15436
PHAROS:  Q15436
GTEx:  ENSG00000100934 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15436
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SEC24 related gene family, member D770Homo sapiensMutation(s): 0 
Gene Names: SEC24D
UniProt & NIH Common Fund Data Resources
Find proteins for O94855 (Homo sapiens)
Explore O94855 
Go to UniProtKB:  O94855
PHAROS:  O94855
GTEx:  ENSG00000150961 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94855
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide7N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13190 (Homo sapiens)
Explore Q13190 
Go to UniProtKB:  Q13190
PHAROS:  Q13190
GTEx:  ENSG00000162236 
Entity Groups  
UniProt GroupQ13190
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.06α = 90
b = 140.83β = 90
c = 152.25γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance