Crystal structure of the tetrameric GTP/dATP/ATP-bound SAMHD1 (RN206) mutant catalytic core

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural Basis of Allosteric Activation of Sterile alpha Motif and Histidine-Aspartate Domain-containing Protein 1 (SAMHD1) by Nucleoside Triphosphates.

Koharudin, L.M.Wu, Y.DeLucia, M.Mehrens, J.Gronenborn, A.M.Ahn, J.

(2014) J Biol Chem 289: 32617-32627

  • DOI: https://doi.org/10.1074/jbc.M114.591958
  • Primary Citation of Related Structures:  
    4QFX, 4QFY, 4QFZ, 4QG0, 4QG1, 4QG2, 4QG4

  • PubMed Abstract: 

    Sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) plays a critical role in inhibiting HIV infection, curtailing the pool of dNTPs available for reverse transcription of the viral genome. Recent structural data suggested a compelling mechanism for the regulation of SAMHD1 enzymatic activity and revealed dGTP-induced association of two inactive dimers into an active tetrameric enzyme. Here, we present the crystal structures of SAMHD1 catalytic core (residues 113-626) tetramers, complexed with mixtures of nucleotides, including dGTP/dATP, dGTP/dCTP, dGTP/dTTP, and dGTP/dUTP. The combined structural and biochemical data provide insight into dNTP promiscuity at the secondary allosteric site and how enzymatic activity is modulated. In addition, we present biochemical analyses of GTP-induced SAMHD1 full-length tetramerization and the structure of SAMHD1 catalytic core tetramer in complex with GTP/dATP, revealing the structural basis of GTP-mediated SAMHD1 activation. Altogether, the data presented here advance our understanding of SAMHD1 function during cellular homeostasis.

  • Organizational Affiliation

    From the Department of Structural Biology and Pittsburgh Center for HIV-Host Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260 amg100@pitt.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
A, B, C, D
550Homo sapiensMutation(s): 2 
Gene Names: SAMHD1MOP5
EC: 3.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3Z3 (Homo sapiens)
Explore Q9Y3Z3 
Go to UniProtKB:  Q9Y3Z3
GTEx:  ENSG00000101347 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3Z3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GTP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
J [auth B],
O [auth D]
C10 H16 N5 O14 P3
Query on DTP

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
L [auth C],
N [auth D]
C10 H16 N5 O12 P3
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth C],
P [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.23α = 90
b = 147.005β = 114.6
c = 99.292γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2014-12-03
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description