6ZGA

COPII on membranes, inner coat


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the complete, membrane-assembled COPII coat reveals a complex interaction network.

Hutchings, J.Stancheva, V.G.Brown, N.R.Cheung, A.C.M.Miller, E.A.Zanetti, G.

(2021) Nat Commun 12: 2034-2034

  • DOI: https://doi.org/10.1038/s41467-021-22110-6
  • Primary Citation of Related Structures:  
    6ZG5, 6ZG6, 6ZGA, 6ZL0

  • PubMed Abstract: 

    COPII mediates Endoplasmic Reticulum to Golgi trafficking of thousands of cargoes. Five essential proteins assemble into a two-layer architecture, with the inner layer thought to regulate coat assembly and cargo recruitment, and the outer coat forming cages assumed to scaffold membrane curvature. Here we visualise the complete, membrane-assembled COPII coat by cryo-electron tomography and subtomogram averaging, revealing the full network of interactions within and between coat layers. We demonstrate the physiological importance of these interactions using genetic and biochemical approaches. Mutagenesis reveals that the inner coat alone can provide membrane remodelling function, with organisational input from the outer coat. These functional roles for the inner and outer coats significantly move away from the current paradigm, which posits membrane curvature derives primarily from the outer coat. We suggest these interactions collectively contribute to coat organisation and membrane curvature, providing a structural framework to understand regulatory mechanisms of COPII trafficking and secretion.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College, London, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC23
A, E
767Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P15303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15303 
Go to UniProtKB:  P15303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15303
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC24
B, F
926Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEC24ANU1YIL109C
Membrane Entity: Yes 
UniProt
Find proteins for P40482 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40482 
Go to UniProtKB:  P40482
Entity Groups  
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UniProt GroupP40482
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small COPII coat GTPase SAR1190Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.5
Membrane Entity: Yes 
UniProt
Find proteins for P20606 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20606 
Go to UniProtKB:  P20606
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20606
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PRO-PRO-PRO
D, H
3Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small COPII coat GTPase SAR1189Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.5
Membrane Entity: Yes 
UniProt
Find proteins for P20606 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20606 
Go to UniProtKB:  P20606
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20606
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
K [auth C],
O [auth G]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
M [auth E],
N [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth C],
P [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONDynamo
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T002670/1
European Research Council (ERC)United Kingdom852915 CRYTOCOP

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references