4EMZ

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 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nsmb.2328
  • Structures With Same Primary Citation

  • 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 ( ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein Nef
B, C
206Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: nef
Find proteins for Q90VU7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q90VU7
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC-I
D, E
28Homo sapiensMutation(s): 0 
Gene Names: HLA-2HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit mu-1
A, M
266Mus musculusMutation(s): 0 
Gene Names: Ap1m1Cltnm
Find proteins for P35585 (Mus musculus)
Go to UniProtKB:  P35585
Protein Feature View
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B,CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • 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

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-04-12 
  • Released Date: 2012-06-20 
  • Deposition Author(s): Jia, X., Xiong, Y.

Revision History 

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references