9RTY | pdb_00009rty

Mammalian AP3 complex on tubular membranes (ARF1 centered Beta3-ARF1 dimer-Delta interface)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

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

Validation slider image for 9RTY

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: 682.35 kDa 
  • Atom Count: 18,000 
  • Modeled Residue Count: 4,500 
  • Deposited Residue Count: 6,030 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-3 complex subunit betaA [auth b],
G [auth B]
658Pan 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
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-3 complex subunit deltaB [auth d],
H [auth D]
1,203Homo sapiensMutation(s): 0 
Gene Names: AP3D1
UniProt & NIH Common Fund Data Resources
Find proteins for A0A8V8TQW4 (Homo sapiens)
Explore A0A8V8TQW4 
Go to UniProtKB:  A0A8V8TQW4
GTEx:  ENSG00000065000 
Entity Groups
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UniProt GroupA0A8V8TQW4
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 1181Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-3 complex subunit mu-1E [auth m],
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-1F [auth s],
N [auth S]
193Homo sapiensMutation(s): 0 
Gene Names: AP3S1CLAPS3
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: 8.90 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

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
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