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 9RTW | pdb_00009rtw

Mammalian AP3 complex on tubular membranes (AP3 centered)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.40 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

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

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This is version 1.0 of the entry. See complete history. 

Literature

Architecture of clathrin-independent AP3:ARF1-coated carriers.

Kaufman, J.G.G., Tagiltsev, G., Stalder, D.S., Taylor, R.J., Sava, I., Guo, H., Ciazynska, K.A., Zaccai, N.R., Gray, S.R., Vallis, Y., Honing, S., Kelly, B.T., Gershlick, D.C., Briggs, J.A.G., Owen, D.J.

(2026) Sci Adv 12: eaed1529-eaed1529

  • DOI: https://doi.org/10.1126/sciadv.aed1529
  • Primary Citation Related Structures: 
    9RTW, 9RTX, 9RTY, 9RTZ

  • PubMed Abstract: 

    The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. AP3 is generally believed to localize to clathrin-free, ARF1-positive, elongated carriers in cells, but the architecture of AP3-based coats was unknown. Using in vitro reconstitution and cryo-electron tomography, we demonstrate that AP3:ARF1 spontaneously remodels membranes containing cargo and the phosphoinositide PI(3,5)P 2 into tubular structures coated in spiraling rows of AP3 arches and ARF1 dimers. Targeted point mutations disrupting critical AP3:ARF1 and AP3:AP3 lattice interfaces disrupt AP3 recruitment, carrier formation, and lysosomal cargo trafficking in cells. We propose that AP3 generates tubular carriers on endosomes by organizing ARF1 dimers into elongated membrane-deforming arrays while simultaneously selecting cargo. By demonstrating that AP3:ARF1 can generate carriers without using a clathrin lattice, we explain the clathrin independence of AP3-mediated trafficking.


  • Organizational Affiliation: 
    • Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.

Macromolecule Content 

  • Total Structure Weight: 274.44 kDa 
  • Atom Count: 9,669 
  • Modeled Residue Count: 2,417 
  • Deposited Residue Count: 2,417 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-3 complex subunit betaA [auth B]563Pan troglodytesMutation(s): 0 
Gene Names: AP3B1
UniProt
Find proteins for A0A2I3SW12 (Pan troglodytes)
Explore A0A2I3SW12 
Go to UniProtKB:  A0A2I3SW12
Entity Groups
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UniProt GroupA0A2I3SW12
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-3 complex subunit delta-1B [auth D]615Homo sapiensMutation(s): 0 
Gene Names: AP3D1, PRO0039
UniProt & NIH Common Fund Data Resources
Find proteins for O14617 (Homo sapiens)
Explore O14617 
Go to UniProtKB:  O14617
PHAROS:  O14617
GTEx:  ENSG00000065000 
Entity Groups
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UniProt GroupO14617
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 1C [auth E],
D [auth F],
E [auth G],
F [auth H]
167Homo sapiensMutation(s): 0 
Gene Names: ARF1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P84077 (Homo sapiens)
Explore P84077 
Go to UniProtKB:  P84077
PHAROS:  P84077
GTEx:  ENSG00000143761 
Entity Groups
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UniProt GroupP84077
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-3 complex subunit mu-1G [auth M]418Rattus norvegicusMutation(s): 0 
Gene Names: Ap3m1
UniProt
Find proteins for A6KKR5 (Rattus norvegicus)
Explore A6KKR5 
Go to UniProtKB:  A6KKR5
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UniProt GroupA6KKR5
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-3 complex subunit sigma-1H [auth S]153Homo sapiensMutation(s): 0 
Gene Names: AP3S1, CLAPS3
UniProt & NIH Common Fund Data Resources
Find proteins for Q92572 (Homo sapiens)
Explore Q92572 
Go to UniProtKB:  Q92572
PHAROS:  Q92572
GTEx:  ENSG00000177879 
Entity Groups
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UniProt GroupQ92572
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.40 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTCoot

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom227915/Z/23/Z
Wellcome TrustUnited Kingdom207455/Z/17/Z
Max Planck SocietyGermany--
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/16
Medical Research Council (MRC, United Kingdom)United KingdomMR/N013433/1
European Molecular Biology Organization (EMBO)European UnionALTF-383-2022
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/W005905/
UK Research and Innovation (UKRI)United KingdomUKRI715
Wellcome TrustUnited Kingdom210481

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release