7P3Z

Homology model of the full-length AP-3 complex in a stretched open conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Flexible open conformation of the AP-3 complex explains its role in cargo recruitment at the Golgi.

Schoppe, J.Schubert, E.Apelbaum, A.Yavavli, E.Birkholz, O.Stephanowitz, H.Han, Y.Perz, A.Hofnagel, O.Liu, F.Piehler, J.Raunser, S.Ungermann, C.

(2021) J Biol Chem 297: 101334-101334

  • DOI: https://doi.org/10.1016/j.jbc.2021.101334
  • Primary Citation of Related Structures:  
    7P3X, 7P3Y, 7P3Z

  • PubMed Abstract: 

    Vesicle formation at endomembranes requires the selective concentration of cargo by coat proteins. Conserved adapter protein complexes at the Golgi (AP-3), the endosome (AP-1), or the plasma membrane (AP-2) with their conserved core domain and flexible ear domains mediate this function. These complexes also rely on the small GTPase Arf1 and/or specific phosphoinositides for membrane binding. The structural details that influence these processes, however, are still poorly understood. Here we present cryo-EM structures of the full-length stable 300 kDa yeast AP-3 complex. The structures reveal that AP-3 adopts an open conformation in solution, comparable to the membrane-bound conformations of AP-1 or AP-2. This open conformation appears to be far more flexible than AP-1 or AP-2, resulting in compact, intermediate, and stretched subconformations. Mass spectrometrical analysis of the cross-linked AP-3 complex further indicates that the ear domains are flexibly attached to the surface of the complex. Using biochemical reconstitution assays, we also show that efficient AP-3 recruitment to the membrane depends primarily on cargo binding. Once bound to cargo, AP-3 clustered and immobilized cargo molecules, as revealed by single-molecule imaging on polymer-supported membranes. We conclude that its flexible open state may enable AP-3 to bind and collect cargo at the Golgi and could thus allow coordinated vesicle formation at the trans-Golgi upon Arf1 activation.


  • Organizational Affiliation

    Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP-3 complex subunit delta964Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5975
UniProt
Find proteins for Q08951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q08951
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UniProt GroupQ08951
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Y55_G0035830.mRNA.1.CDS.1809Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2762
UniProt
Find proteins for P46682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46682 
Go to UniProtKB:  P46682
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UniProt GroupP46682
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AP-3 complex subunit muC [auth M]483Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38153 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38153
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP complex subunit sigmaD [auth S]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS3239PACBIOSEQ_LOCUS3310SCNYR20_0009016500SCP684_0009016000
UniProt
Find proteins for P47064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47064 
Go to UniProtKB:  P47064
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UniProt GroupP47064
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPHIRE1.3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRA1781/2-4

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.3: 2021-12-08
    Changes: Database references