4EMZ | pdb_00004emz

HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef.

Jia, X.Singh, R.Homann, S.Yang, H.Guatelli, J.Xiong, Y.

(2012) Nat Struct Mol Biol 19: 701-706

  • DOI: https://doi.org/10.1038/nsmb.2328
  • Primary Citation Related Structures: 
    4EMZ, 4EN2

  • PubMed Abstract: 

    The HIV-1 protein Nef inhibits antigen presentation by class I major histocompatibility complex (MHC-I). We determined the mechanism of this activity by solving the crystal structure of a protein complex comprising Nef, the MHC-I cytoplasmic domain (MHC-I CD) and the μ1 subunit of the clathrin adaptor protein complex 1. A ternary, cooperative interaction clamps the MHC-I CD into a narrow binding groove at the Nef-μ1 interface, which encompasses the cargo-recognition site of μ1 and the proline-rich strand of Nef. The Nef C terminus induces a previously unobserved conformational change in μ1, whereas the N terminus binds the Nef core to position it optimally for complex formation. Positively charged patches on μ1 recognize acidic clusters in Nef and MHC-I. The structure shows how Nef functions as a clathrin-associated sorting protein to alter the specificity of host membrane trafficking and enable viral evasion of adaptive immunity.


  • Organizational Affiliation
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

Macromolecule Content 

  • Total Structure Weight: 114.36 kDa 
  • Atom Count: 6,789 
  • Modeled Residue Count: 826 
  • Deposited Residue Count: 1,000 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein NefA [auth C],
D [auth B]
206Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: nef
UniProt
Find proteins for Q90VU7 (Human immunodeficiency virus type 1)
Explore Q90VU7 
Go to UniProtKB:  Q90VU7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90VU7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC-IB [auth D],
C [auth E]
28Homo sapiensMutation(s): 0 
Gene Names: HLA-2
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-1 complex subunit mu-1E [auth A],
F [auth M]
266Mus musculusMutation(s): 0 
Gene Names: Ap1m1Cltnm
UniProt
Find proteins for P35585 (Mus musculus)
Explore P35585 
Go to UniProtKB:  P35585
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35585
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth C],
D [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.324α = 90
b = 112.471β = 90
c = 114.407γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary