6DFF

Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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, Nef protein chimeraA [auth L],
B [auth T]
264Homo sapiensHuman immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
Gene Names: BST2nef
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PHAROS:  Q10589
GTEx:  ENSG00000130303 
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UniProt GroupsQ90VU7Q10589
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit beta-1C [auth B]586Homo sapiensMutation(s): 2 
Gene Names: AP1B1ADTB1BAM22CLAPB2
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PHAROS:  Q10567
GTEx:  ENSG00000100280 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylation factor 1D [auth C],
F [auth H]
193Homo sapiensMutation(s): 1 
Gene Names: ARF1
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PHAROS:  P84077
GTEx:  ENSG00000143761 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit gamma-1E [auth G]601Mus musculusMutation(s): 0 
Gene Names: Ap1g1AdtgClapg1
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IMPC:  MGI:101919
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit mu-1G [auth M]423Mus musculusMutation(s): 0 
Gene Names: Ap1m1Cltnm
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit sigma-3H [auth S]154Homo sapiensMutation(s): 0 
Gene Names: AP1S3
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GTEx:  ENSG00000152056 
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
I [auth C],
K [auth H]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth C],
L [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 General Medical Sciences (NIH/NIGMS)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, Other