4Z8L

Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Clade-specific Engagement of SAMHD1 (Sterile alpha Motif and Histidine/Aspartate-containing Protein 1) Restriction Factors by Lentiviral Viral Protein X (Vpx) Virulence Factors.

Wu, Y.Koharudin, L.M.Mehrens, J.DeLucia, M.Byeon, C.H.Byeon, I.J.Calero, G.Ahn, J.Gronenborn, A.M.

(2015) J.Biol.Chem. 290: 17935-17945

  • DOI: 10.1074/jbc.M115.665513

  • PubMed Abstract: 
  • Sterile α motif (SAM) and histidine/aspartate (HD)-containing protein 1 (SAMHD1) restricts human/simian immunodeficiency virus infection in certain cell types and is counteracted by the virulence factor Vpx. Current evidence indicates that Vpx recrui ...

    Sterile α motif (SAM) and histidine/aspartate (HD)-containing protein 1 (SAMHD1) restricts human/simian immunodeficiency virus infection in certain cell types and is counteracted by the virulence factor Vpx. Current evidence indicates that Vpx recruits SAMHD1 to the Cullin4-Ring Finger E3 ubiquitin ligase (CRL4) by facilitating an interaction between SAMHD1 and the substrate receptor DDB1- and Cullin4-associated factor 1 (DCAF1), thereby targeting SAMHD1 for proteasome-dependent down-regulation. Host-pathogen co-evolution and positive selection at the interfaces of host-pathogen complexes are associated with sequence divergence and varying functional consequences. Two alternative interaction interfaces are used by SAMHD1 and Vpx: the SAMHD1 N-terminal tail and the adjacent SAM domain or the C-terminal tail proceeding the HD domain are targeted by different Vpx variants in a unique fashion. In contrast, the C-terminal WD40 domain of DCAF1 interfaces similarly with the two above complexes. Comprehensive biochemical and structural biology approaches permitted us to delineate details of clade-specific recognition of SAMHD1 by lentiviral Vpx proteins. We show that not only the SAM domain but also the N-terminal tail engages in the DCAF1-Vpx interaction. Furthermore, we show that changing the single Ser-52 in human SAMHD1 to Phe, the residue found in SAMHD1 of Red-capped monkey and Mandrill, allows it to be recognized by Vpx proteins of simian viruses infecting those primate species, which normally does not target wild type human SAMHD1 for degradation.


    Organizational Affiliation

    From the Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein VPRBP
A, D
349Homo sapiensGene Names: VPRBP (DCAF1, KIAA0800, RIP)
EC: 2.7.11.1
Find proteins for Q9Y4B6 (Homo sapiens)
Go to UniProtKB:  Q9Y4B6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vpx protein
B, E
100Simian immunodeficiency virusGene Names: vpx
Find proteins for Q7ZB17 (Simian immunodeficiency virus)
Go to UniProtKB:  Q7ZB17
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SAM domain and HD domain-containing protein
C, F
118Mandrillus sphinxGene Names: SAMHD1
Find proteins for H6WEA4 (Mandrillus sphinx)
Go to Gene View: SAMHD1
Go to UniProtKB:  H6WEA4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 74.490α = 90.00
b = 74.490β = 90.00
c = 178.180γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50GM82251

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-29
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy