8D9S image
Entry Detail
PDB ID:
8D9S
EMDB ID:
Title:
AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1
Biological Source:
PDB Version:
Deposition Date:
2022-06-11
Release Date:
2022-11-09
Method Details:
Experimental Method:
Resolution:
20.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SUBTOMOGRAM AVERAGING
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:AP-1 complex subunit beta-1
Mutations:K359R,E476K
Chain IDs:E (auth: B), O (auth: A), Y (auth: D), IA (auth: E), SA (auth: F), CB (auth: I)
Chain Length:949
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:ADP ribosylation factor 1
Chain IDs:A (auth: C), B (auth: H), J (auth: Z), K (auth: J), L (auth: X), T (auth: 3), U (auth: K), V (auth: a), DA (auth: 4), EA (auth: O), FA (auth: b), NA (auth: 5), OA (auth: P), PA (auth: c), XA (auth: 6), YA (auth: Q), ZA (auth: d), HB (auth: 7)
Chain Length:181
Number of Molecules:18
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:AP-1 complex subunit gamma-1
Chain IDs:F (auth: G), P (auth: R), Z (auth: T), JA (auth: U), TA (auth: V), DB (auth: W)
Chain Length:601
Number of Molecules:6
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:AP-1 complex subunit mu-1
Chain IDs:H (auth: M), R (auth: j), BA (auth: k), LA (auth: l), VA (auth: m), FB (auth: n)
Chain Length:181
Number of Molecules:6
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Protein Nef
Chain IDs:C (auth: N), G (auth: L), M (auth: o), Q (auth: e), W (auth: p), AA (auth: f), GA (auth: q), KA (auth: g), QA (auth: r), UA (auth: h), AB (auth: s), EB (auth: i)
Chain Length:949
Number of Molecules:12
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Description:AP-1 complex subunit sigma-3
Chain IDs:I (auth: S), S (auth: t), CA (auth: u), MA (auth: v), WA (auth: w), GB (auth: x)
Chain Length:213
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:HLA class I histocompatibility antigen, A alpha chain
Mutations:T345S, S349G, G355S, C363A
Chain IDs:D (auth: Y), N (auth: y), X (auth: z), HA (auth: 0), RA (auth: 1), BB (auth: 2)
Chain Length:44
Number of Molecules:6
Biological Source:Homo sapiens
Primary Citation
Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat.
Sci Adv 8 eadd3914 eadd3914 (2022)
PMID: 36269825 DOI: 10.1126/sciadv.add3914

Abstact

The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester major histocompatibility complex class I (MHC-I), evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes without clathrin and determined its structure. The coat assembles via Arf1 dimer interfaces. AP-1-positive tubules are enriched in cells upon clathrin knockdown. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact residues are conserved across Arf isoforms and the Arf-dependent AP complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with Arf1 into tubular coats without clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats as an intermediate in clathrin vesicle formation from internal membranes and as an MHC-I sequestration mechanism in HIV-1 infection.

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