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: 2.7 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: 10.1038/emboj.2008.208
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec23A
A
765Homo sapiensMutation(s): 0 
Gene Names: SEC23A
Find proteins for Q15436 (Homo sapiens)
Go to Gene View: SEC23A
Go to UniProtKB:  Q15436
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SEC24 related gene family, member D
B
770Homo sapiensMutation(s): 0 
Gene Names: SEC24D (KIAA0755)
Find proteins for O94855 (Homo sapiens)
Go to Gene View: SEC24D
Go to UniProtKB:  O94855
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide
C
7Homo sapiensMutation(s): 0 
Gene Names: STX5 (STX5A)
Find proteins for Q13190 (Homo sapiens)
Go to Gene View: STX5
Go to UniProtKB:  Q13190
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 103.060α = 90.00
b = 140.830β = 90.00
c = 152.250γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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