3U1N

Structure of the catalytic core of human SAMHD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase

Goldstone, D.C.Ennis-Adeniran, V.Hedden, J.J.Groom, H.C.Rice, G.I.Christodoulou, E.Walker, P.A.Kelly, G.Haire, L.F.Yap, M.W.de Carvalho, L.P.Stoye, J.P.Crow, Y.J.Taylor, I.A.Webb, M.

(2011) Nature 480: 379-382

  • DOI: 10.1038/nature10623

  • PubMed Abstract: 
  • SAMHD1, an analogue of the murine interferon (IFN)-γ-induced gene Mg11 (ref. 1), has recently been identified as a human immunodeficiency virus-1 (HIV-1) restriction factor that blocks early-stage virus replication in dendritic and other myeloid cell ...

    SAMHD1, an analogue of the murine interferon (IFN)-γ-induced gene Mg11 (ref. 1), has recently been identified as a human immunodeficiency virus-1 (HIV-1) restriction factor that blocks early-stage virus replication in dendritic and other myeloid cells and is the target of the lentiviral protein Vpx, which can relieve HIV-1 restriction. SAMHD1 is also associated with Aicardi-Goutières syndrome (AGS), an inflammatory encephalopathy characterized by chronic cerebrospinal fluid lymphocytosis and elevated levels of the antiviral cytokine IFN-α. The pathology associated with AGS resembles congenital viral infection, such as transplacentally acquired HIV. Here we show that human SAMHD1 is a potent dGTP-stimulated triphosphohydrolase that converts deoxynucleoside triphosphates to the constituent deoxynucleoside and inorganic triphosphate. The crystal structure of the catalytic core of SAMHD1 reveals that the protein is dimeric and indicates a molecular basis for dGTP stimulation of catalytic activity against dNTPs. We propose that SAMHD1, which is highly expressed in dendritic cells, restricts HIV-1 replication by hydrolysing the majority of cellular dNTPs, thus inhibiting reverse transcription and viral complementary DNA (cDNA) synthesis.


    Organizational Affiliation

    Division of Molecular Structure, MRC National Institute for Medical Research, London NW7 1AA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SAM domain and HD domain-containing protein 1
A, B, C, D
528Homo sapiensMutation(s): 0 
Gene Names: SAMHD1 (MOP5)
EC: 3.1.5.-
Find proteins for Q9Y3Z3 (Homo sapiens)
Go to Gene View: SAMHD1
Go to UniProtKB:  Q9Y3Z3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 81.516α = 91.18
b = 95.818β = 109.24
c = 96.661γ = 115.20
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
RESOLVEphasing
SHELXphasing
SHELXDphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-12-14
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2018-01-24
    Type: Structure summary