Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - A4B2C2D2E1F1G1H1I1J1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A4B4C2D2E1F1G1H1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1,033.07 kDa 
• Atom Count: 27,895 
• Modelled Residue Count: 6,978 
• Deposited Residue Count: 9,164 
• Unique protein chains: 8

 5NZT

The structure of the COPI coat linkage I

• PDB DOI:  https://doi.org/10.2210/pdb5NZT/pdb
• EM Map EMD-3722: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus, Saccharomyces cerevisiae
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-15 Released: 2017-06-28 
• Deposition Author(s): Dodonova, S.O., Aderhold, P., Kopp, J., Ganeva, I., Roehling, S., Hagen, W.J.H., Sinning, I., Wieland, F., Briggs, J.A.G.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 17.0 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

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

• PubMed: 28621666 
• 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.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit alpha	A	1,262	Mus musculus	Mutation(s): 0  Gene Names: Copa
UniProt
Find proteins for Q8CIE6 (Mus musculus) Explore Q8CIE6  Go to UniProtKB:  Q8CIE6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit epsilon	B [auth E]	308	Mus musculus	Mutation(s): 0  Gene Names: Cope, Cope1
UniProt
Find proteins for O89079 (Mus musculus) Explore O89079  Go to UniProtKB:  O89079

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit beta	C [auth B], M [auth N]	968	Mus musculus	Mutation(s): 0  Gene Names: Copb1, Copb
UniProt
Find proteins for Q9JIF7 (Mus musculus) Explore Q9JIF7  Go to UniProtKB:  Q9JIF7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit beta'	D [auth C], N [auth H]	905	Mus musculus	Mutation(s): 0  Gene Names: Copb2
UniProt & NIH Common Fund Data Resources
Find proteins for O55029 (Mus musculus) Explore O55029  Go to UniProtKB:  O55029
IMPC:  MGI:1354962

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit delta	E [auth D], O [auth I]	511	Mus musculus	Mutation(s): 0  Gene Names: Arcn1, Copd
UniProt & NIH Common Fund Data Resources
Find proteins for Q5XJY5 (Mus musculus) Explore Q5XJY5  Go to UniProtKB:  Q5XJY5
IMPC:  MGI:2387591

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 1	F, H [auth R], L [auth M], P [auth J]	181	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ARF1, YDL192W, D1244
UniProt
Find proteins for P11076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11076  Go to UniProtKB:  P11076

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit gamma-1	G, J [auth K]	874	Mus musculus	Mutation(s): 0  Gene Names: Copg1, Copg
UniProt
Find proteins for Q9QZE5 (Mus musculus) Explore Q9QZE5  Go to UniProtKB:  Q9QZE5

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit zeta-1	I [auth Z], K [auth L]	177	Mus musculus	Mutation(s): 0  Gene Names: Copz1, Copz
UniProt
Find proteins for P61924 (Mus musculus) Explore P61924  Go to UniProtKB:  P61924

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 17.0 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	TOM Toolbox
RECONSTRUCTION	AV3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Dodonova, S.O., Aderhold, P., Kopp, J., Ganeva, I., Roehling, S., Hagen, W.J.H., Sinning, I., Wieland, F., Briggs, J.A.G.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB638 (A16 and Z4)
German Research Foundation	Germany	WI 654/12-1

Revision History  

• 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: Advisory, Data processing
• Version 1.3: 2018-10-24
  Changes: Advisory, Data collection, Derived calculations