9QPQ | pdb_00009qpq

The structure of the COPI leaf bound to GOLPH3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Models: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The mechanistic basis of cargo selection during Golgi maturation.

Taylor, R.J.Zubkov, N.Ciazynska, K.A.Kaufman, J.G.G.Tagiltsev, G.Owen, D.J.Briggs, J.A.G.Munro, S.

(2025) Sci Adv 11: eaea0016-eaea0016

  • DOI: https://doi.org/10.1126/sciadv.aea0016
  • Primary Citation of Related Structures:  
    9QPQ

  • PubMed Abstract: 

    The multiple cisternae of the Golgi apparatus contain resident membrane proteins crucial for lipid and protein glycosylation. How Golgi residents remain in their designated compartments despite a constant flow of secretory cargo is incompletely understood. Here, we determine the structure of the COPI vesicle coat containing GOLPH3, an adaptor protein that binds the cytosolic tails of many Golgi residents. Analysis of this structure, together with structure-guided mutagenesis and functional assays, reveals how GOLPH3 uses coincidence detection of COPI and lipids to engage Golgi residents preferentially at late cisternae. Our findings rationalize the logic of cisternal maturation and explain how COPI can engage different types of substrates in different Golgi cisternae to retrieve some proteins back to the ER while retaining others within the Golgi apparatus.


  • Organizational Affiliation
    • Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, 82512, Germany.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Golgi phosphoprotein 3
A, B
298Homo sapiensMutation(s): 0 
Gene Names: GOLPH3GPP34
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PHAROS:  Q9H4A6
GTEx:  ENSG00000113384 
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UniProt GroupQ9H4A6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit alphaC [auth D],
D [auth E]
1,224Mus musculusMutation(s): 0 
Gene Names: Copa
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit beta'E [auth F],
F [auth G]
905Mus musculusMutation(s): 0 
Gene Names: Copb2
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IMPC:  MGI:1354962
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit betaG [auth H],
H [auth I],
I [auth J],
J [auth K]
953Mus musculusMutation(s): 0 
Gene Names: Copb1Copb
UniProt
Find proteins for Q9JIF7 (Mus musculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit deltaK [auth L]511Mus musculusMutation(s): 0 
Gene Names: Arcn1Copd
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IMPC:  MGI:2387591
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit gamma-1L [auth M],
M [auth N],
N [auth O]
874Mus musculusMutation(s): 0 
Gene Names: Copg1Copg
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit zeta-1O [auth P]177Mus musculusMutation(s): 0 
Gene Names: Copz1Copz
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 1P [auth R],
Q [auth S],
R [auth T]
181Homo sapiensMutation(s): 0 
Gene Names: ARF1
EC: 3.6.5.2
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PHAROS:  P84077
GTEx:  ENSG00000143761 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELIONv3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105178783
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/16
Wellcome TrustUnited Kingdom227915/Z/23/Z
European Molecular Biology Organization (EMBO)European UnionALTF-383-2022

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release