5AO4 | pdb_00005ao4

Crystal structure of in vitro phosphorylated human SAMHD1 (amino acid residues 115-626) bound to GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.308 (Depositor), 0.311 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction.

Arnold, L.H.Groom, H.C.T.Kunzelmann, S.Schwefel, D.Caswell, S.J.Ordonez, P.Mann, M.C.Rueschenbaum, S.Goldstone, D.C.Pennell, S.Howell, S.A.Stoye, J.P.Webb, M.Taylor, I.A.Bishop, K.N.

(2015) PLoS Pathog 11: 5194

  • DOI: https://doi.org/10.1371/journal.ppat.1005194
  • Primary Citation Related Structures: 
    5AO0, 5AO1, 5AO2, 5AO3, 5AO4

  • PubMed Abstract: 

    SAMHD1 restricts HIV-1 infection of myeloid-lineage and resting CD4+ T-cells. Most likely this occurs through deoxynucleoside triphosphate triphosphohydrolase activity that reduces cellular dNTP to a level where reverse transcriptase cannot function, although alternative mechanisms have been proposed recently. Here, we present combined structural and virological data demonstrating that in addition to allosteric activation and triphosphohydrolase activity, restriction correlates with the capacity of SAMHD1 to form "long-lived" enzymatically competent tetramers. Tetramer disruption invariably abolishes restriction but has varied effects on in vitro triphosphohydrolase activity. SAMHD1 phosphorylation also ablates restriction and tetramer formation but without affecting triphosphohydrolase steady-state kinetics. However phospho-SAMHD1 is unable to catalyse dNTP turnover under conditions of nucleotide depletion. Based on our findings we propose a model for phosphorylation-dependent regulation of SAMHD1 activity where dephosphorylation switches housekeeping SAMHD1 found in cycling cells to a high-activity stable tetrameric form that depletes and maintains low levels of dNTPs in differentiated cells.


  • Organizational Affiliation
    • The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 251.41 kDa 
  • Atom Count: 12,222 
  • Modeled Residue Count: 1,625 
  • Deposited Residue Count: 2,152 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
A, B, C, D
538Homo sapiensMutation(s): 0 
EC: 3.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3Z3 (Homo sapiens)
Explore Q9Y3Z3 
Go to UniProtKB:  Q9Y3Z3
PHAROS:  Q9Y3Z3
GTEx:  ENSG00000101347 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3Z3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
J [auth C],
L [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
I [auth C],
K [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.308 (Depositor), 0.311 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.545α = 90
b = 80.817β = 114.93
c = 147.665γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Data collection
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary