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

Abstract
Data availability
Article and author information
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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.

Data availability

The following data sets were generated

1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat leaf
EMD-3720.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-3720
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat leaf in complex with the ArfGAP2 uncoating factor
EMD-3721.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-3721
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat linkage I
EMD-3722.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-3722
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat linkage II
EMD-3723.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-3723
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat linkage IV
EMD-3724.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-3724
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat leaf
5NZR.

http://www.ebi.ac.uk/pdbe/entry/pdb/5NZR
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat leaf in complex with the ArfGAP2 uncoating factor
5NZS.

http://www.ebi.ac.uk/pdbe/entry/pdb/5NZS
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat linkage I
5NZT.

http://www.ebi.ac.uk/pdbe/entry/pdb/5NZT
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat linkage II
5NZU.

http://www.ebi.ac.uk/pdbe/entry/pdb/5NZU
1. Dodonova
2. S.O. Aderhold
3. P. Kopp
4. J. Ganeva
5. I. Röhling
6. S. Hagen
7. W.J.H. Sinning
8. I. Wieland
9. W. Briggs
10. J.A.G.
(2017) The structure of the COPI coat linkage IV
5NZV.

http://www.ebi.ac.uk/pdbe/entry/pdb/5NZV

The following previously published data sets were used

(2015) The structure of the COPI coat triad
EMD-2985.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2985
1. Ma
2. W. Goldberg
3. J.
(2013) Crystal structure of alpha-COP
4J87.

http://www.ebi.ac.uk/pdbe/entry/pdb/4J87
1. Amor
2. J. C. Harrison
3. D. H. Kahn
4. R. A. Ringe
5. D.
(1994) Saccharomyces cerevisiae ADP-ribosylation Factor 2 (ScArf2) complexed with GDP-3'P at 1.6A resolution
1MR3.

http://www.ebi.ac.uk/pdbe/entry/pdb/1MR3
1. Ismail
2. S. A. Vetter
3. I. R. Sot
4. B. Wittinghofer
5. A.
(2010) The crystal structure of ASAP3 in complex with Arf6 in transition state
3LVQ.

http://www.ebi.ac.uk/pdbe/entry/pdb/3LVQ
1. Yu
2. X. Breitman
3. M. Goldberg
4. J
(2012) Crystal Structure of Arf1 Bound to the gamma/zeta-COP Core Complex
3TJZ.

http://www.ebi.ac.uk/pdbe/entry/pdb/3TJZ
1. Lee
2. C. Goldberg
3. J.
(2010) Crystal structure of yeast alpha/betaprime-COP subcomplex of the COPI vesicular coat
3MKQ.

http://www.ebi.ac.uk/pdbe/entry/pdb/3MKQ
(2003) Structural Identification of a conserved appendage domain in the carboxyl-terminus of the COPI gamma-subunit
1PZD.

http://www.ebi.ac.uk/pdbe/entry/pdb/1PZD
1. Lee
2. C. Goldberg
3. J.
(2010) Crystal structure of yeast alpha/epsilon-COP subcomplex of the COPI vesicular coat
3MKR.

http://www.ebi.ac.uk/pdbe/entry/pdb/3MKR
1. Hsia
2. K. Hoelz
3. A.
(2010) Crystal Structure of a-COP in Complex with e-COP
3MV2.

http://www.ebi.ac.uk/pdbe/entry/pdb/3MV2
1. Lahav
2. A. Rozenberg
3. H. Parnis
4. A. Cassel
5. D. Adir
6. N.
(2015) Crystal structure of bovine MHD domain of the COPI delta subunit at 2.15 A resolution
4O8Q.

http://www.ebi.ac.uk/pdbe/entry/pdb/4O8Q
1. Jackson
2. L. P. Kelly
3. B. T. McCoy
4. A. J. Gaffry
5. T. James
6. L. C. Collins
7. B. M. Honing
8. S. Evans
9. P. R. Owen
10. D. J.
(2010) AP2 CLATHRIN ADAPTOR CORE IN ACTIVE COMPLEX WITH CARGO PEPTIDES
2XA7.

http://www.ebi.ac.uk/pdbe/entry/pdb/2XA7
(2006) Beta appendage of AP2 complexed with ARH peptide
2G30.

http://www.ebi.ac.uk/pdbe/entry/pdb/2G30
1. Tong
2. Y. Dimov
3. S. Shen
4. L. Zhu
5. H. Tempel
6. W. Landry
7. R. Arrowsmith
8. C.H. Edwards
9. A.M. Sundstrom
10. M. Weigelt
11. J. Bochkarev
12. A. Park
13. H.
(2007) GAP domain of ZNF289, an ID1-regulated zinc finger protein
2P57.

http://www.ebi.ac.uk/pdbe/entry/pdb/2P57

Article and author information

Author details

Svetlana O Dodonova

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

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5002-8138
Patrick Aderhold

Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany

Competing interests
The authors declare that no competing interests exist.
Juergen Kopp

Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany

Competing interests
The authors declare that no competing interests exist.
Iva Ganeva

Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany

Competing interests
The authors declare that no competing interests exist.
Simone Röhling

Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany

Competing interests
The authors declare that no competing interests exist.
Wim J Hagen

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

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-6229-2692
Irmgard Sinning

Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany

Competing interests
The authors declare that no competing interests exist.
Felix Wieland

Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany

Competing interests
The authors declare that no competing interests exist.
John AG Briggs

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

For correspondence
john.briggs@embl.de

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3990-6910

Funding

Deutsche Forschungsgemeinschaft (SFB638 (A16))

Felix Wieland
John AG Briggs

Deutsche Forschungsgemeinschaft (SFB638 (Z4))

Irmgard Sinning

Deutsche Forschungsgemeinschaft (WI 654/12-1)

Felix Wieland

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

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