5NZT

The structure of the COPI coat linkage I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17 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: 10.7554/eLife.26691
  • Primary Citation of Related Structures:  

  • 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, trigg ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit alpha
A
1262Mus musculusMutation(s): 0 
Gene Names: Copa
Find proteins for Q8CIE6 (Mus musculus)
Go to UniProtKB:  Q8CIE6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit epsilon
E
308Mus musculusMutation(s): 0 
Gene Names: Cope (Cope1)
Find proteins for O89079 (Mus musculus)
Go to UniProtKB:  O89079
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit beta
B, N
968Mus musculusMutation(s): 0 
Gene Names: Copb1 (Copb)
Find proteins for Q9JIF7 (Mus musculus)
Go to UniProtKB:  Q9JIF7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit beta'
C, H
905Mus musculusMutation(s): 0 
Gene Names: Copb2
Find proteins for O55029 (Mus musculus)
Go to UniProtKB:  O55029
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit delta
D, I
511Mus musculusMutation(s): 0 
Gene Names: Arcn1 (Copd)
Find proteins for Q5XJY5 (Mus musculus)
Go to UniProtKB:  Q5XJY5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosylation factor 1
F, R, M, J
181Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARF1
Find proteins for P11076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ARF1
Go to UniProtKB:  P11076
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit gamma-1
G, K
874Mus musculusMutation(s): 0 
Gene Names: Copg1 (Copg)
Find proteins for Q9QZE5 (Mus musculus)
Go to UniProtKB:  Q9QZE5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit zeta-1
Z, L
177Mus musculusMutation(s): 0 
Gene Names: Copz1 (Copz)
Find proteins for P61924 (Mus musculus)
Go to UniProtKB:  P61924
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

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