5NZV

The structure of the COPI coat linkage IV


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17.3 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

9 angstrom structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments.

Dodonova, S.O.Aderhold, P.Kopp, J.Ganeva, I.Rohling, S.Hagen, W.J.Sinning, I.Wieland, F.Briggs, J.A.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.26691
  • Primary Citation of Related Structures:  
    5MU7, 5NZR, 5NZS, 5NZT, 5NZU, 5NZV

  • PubMed Abstract: 

    COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution. We also obtained a 2.57 Å resolution crystal structure of βδ-COP. By combining these structures we built a molecular model of the coat. We additionally determined the coat structure in the presence of ArfGAP proteins that regulate coat dissociation. We found that Arf1 occupies contrasting molecular environments within the coat, leading us to hypothesize that some Arf1 molecules may regulate vesicle assembly while others regulate coat disassembly.


  • Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit alphaA,
M [auth H]
1,262Mus musculusMutation(s): 0 
Gene Names: Copa
UniProt
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UniProt GroupQ8CIE6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit epsilonB [auth E],
N [auth O]
308Mus musculusMutation(s): 0 
Gene Names: CopeCope1
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit betaC [auth B],
O [auth I]
968Mus musculusMutation(s): 0 
Gene Names: Copb1Copb
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit beta'D [auth C],
P [auth J]
905Mus musculusMutation(s): 0 
Gene Names: Copb2
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:1354962
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit deltaE [auth D],
Q [auth N]
511Mus musculusMutation(s): 0 
Gene Names: Arcn1Copd
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IMPC:  MGI:2387591
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 1F,
H [auth R],
L [auth M],
R [auth P],
V [auth T]
181Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ARF1YDL192WD1244
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit gamma-1G,
J [auth K],
T [auth Q]
874Mus musculusMutation(s): 0 
Gene Names: Copg1Copg
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit zeta-1I [auth Z],
K [auth L],
S [auth U],
U [auth S]
177Mus musculusMutation(s): 0 
Gene Names: Copz1Copz
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17.3 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONTOM Toolbox
RECONSTRUCTIONAV3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB638 (A16 and Z4)
German Research FoundationGermanyWI 654/12-1

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence, Data collection, Experimental preparation, Refinement description
  • Version 1.2: 2018-01-31
    Changes: Data processing
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations