3EGX

Crystal structure of the mammalian COPII-coat protein Sec23a/24a complexed with the SNARE protein Sec22b and bound to the transport signal sequence of the SNARE protein Bet1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.206 

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:  
    3EFO, 3EH1, 3EH2, 3EGD, 3EG9, 3EGX

  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein Sec23AA764Homo sapiensMutation(s): 0 
Gene Names: SEC23A
Find proteins for Q15436 (Homo sapiens)
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Go to UniProtKB:  Q15436
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PHAROS:  Q15436
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein Sec24AB748Homo sapiensMutation(s): 0 
Gene Names: SEC24A
Find proteins for O95486 (Homo sapiens)
Explore O95486 
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PHAROS:  O95486
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vesicle-trafficking protein SEC22bC157Homo sapiensMutation(s): 0 
Gene Names: SEC22BSEC22L1
Find proteins for O75396 (Homo sapiens)
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Go to UniProtKB:  O75396
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PHAROS:  O75396
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
9-residue synthetic peptide from SNARE protein Bet1D9N/AMutation(s): 0 
Find proteins for O15155 (Homo sapiens)
Explore O15155 
Go to UniProtKB:  O15155
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PHAROS:  O15155
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.15α = 90
b = 97.23β = 90.01
c = 129.51γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

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