6D84

Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation.

Morris, K.L., Buffalo, C.Z., Sturzel, C.M., Heusinger, E., Kirchhoff, F., Ren, X., Hurley, J.H.

(2018) Cell 174: 659-671.e14

  • DOI: 10.1016/j.cell.2018.07.004
  • Primary Citation of Related Structures:  
    6CM9, 6CRI, 6D83, 6D84, 6DFF

  • PubMed Abstract: 

    • The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention ...

    The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 Å structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.

    Organizational Affiliation: 

    Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jimhurley@berkeley.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bone marrow stromal antigen 2,Protein NefB [auth L], J [auth O], I [auth R], A [auth T]264Homo sapiens, Human immunodeficiency virus 1
This entity is chimeric		Mutation(s): 2 
Gene Names: BST2, nef
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Find proteins for Q90VU7 (Human immunodeficiency virus 1)
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Find proteins for Q10589 (Homo sapiens)
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PHAROS:  Q10589
GTEx:  ENSG00000130303
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit beta-1C [auth B], K [auth F]586Homo sapiensMutation(s): 0 
Gene Names: AP1B1, ADTB1, BAM22, CLAPB2
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Find proteins for Q10567 (Homo sapiens)
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GTEx:  ENSG00000100280
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylation factor 1D [auth C], F [auth H], L [auth I], N193Homo sapiensMutation(s): 0 
Gene Names: ARF1
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Find proteins for P84077 (Homo sapiens)
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GTEx:  ENSG00000143761
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit gamma-1E [auth G], M [auth K]601Mus musculusMutation(s): 0 
Gene Names: Ap1g1, Adtg, Clapg1
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IMPC:  MGI:101919
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit mu-1G [auth M], O [auth P]423Mus musculusMutation(s): 0 
Gene Names: Ap1m1, Cltnm
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit sigma-3P [auth Q], H [auth S]154Homo sapiensMutation(s): 0 
Gene Names: AP1S3
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI 120691

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence