6U3V

Crystal structure of human alpha/epsilon-COP of the COPI vesicular coat bound to alpha-COP STM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering.

Travis, S.M.Kokona, B.Fairman, R.Hughson, F.M.

(2019) Proc Natl Acad Sci U S A 116: 24031-24040

  • DOI: 10.1073/pnas.1909697116
  • Primary Citation of Related Structures:  
    6U3W, 6U3V, 6TZT

  • PubMed Abstract: 
  • Coat protein I (COPI)-coated vesicles mediate retrograde transport from the Golgi to the endoplasmic reticulum (ER), as well as transport within the Golgi. Major progress has been made in defining the structure of COPI coats, in vitro and in vivo, at ...

    Coat protein I (COPI)-coated vesicles mediate retrograde transport from the Golgi to the endoplasmic reticulum (ER), as well as transport within the Golgi. Major progress has been made in defining the structure of COPI coats, in vitro and in vivo, at resolutions as high as 9 Å. Nevertheless, important questions remain unanswered, including what specific interactions stabilize COPI coats, how COPI vesicles recognize their target membranes, and how coat disassembly is coordinated with vesicle fusion and cargo delivery. Here, we use X-ray crystallography to identify a conserved site on the COPI subunit α-COP that binds to flexible, acidic sequences containing a single tryptophan residue. One such sequence, found within α-COP itself, mediates α-COP homo-oligomerization. Another such sequence is contained within the lasso of the ER-resident Dsl1 complex, where it helps mediate the tethering of Golgi-derived COPI vesicles at the ER membrane. Together, our findings suggest that α-COP homo-oligomerization plays a key role in COPI coat stability, with potential implications for the coordination of vesicle tethering, uncoating, and fusion.


    Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ 08544; hughson@princeton.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coatomer subunit epsilonA, C322Homo sapiensMutation(s): 0 
Gene Names: COPE
Find proteins for O14579 (Homo sapiens)
Explore O14579 
Go to UniProtKB:  O14579
NIH Common Fund Data Resources
PHAROS  O14579
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coatomer subunit alphaB, D356Homo sapiensMutation(s): 0 
Gene Names: COPA
Find proteins for P53621 (Homo sapiens)
Explore P53621 
Go to UniProtKB:  P53621
NIH Common Fund Data Resources
PHAROS  P53621
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.103α = 90
b = 138.103β = 90
c = 192.94γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM071574
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF31GM12676
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM007388

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2019-12-11
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence