6TXA | pdb_00006txa

Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dGMPNPP and Mg

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis.

Morris, E.R., Caswell, S.J., Kunzelmann, S., Arnold, L.H., Purkiss, A.G., Kelly, G., Taylor, I.A.

(2020) Nat Commun 11: 3165-3165

  • DOI: https://doi.org/10.1038/s41467-020-16983-2
  • Primary Citation Related Structures: 
    6TX0, 6TXA, 6TXC, 6TXE, 6TXF, 6XU1, 6YOM

  • PubMed Abstract: 

    SAMHD1 regulates cellular 2'-deoxynucleoside-5'-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2'-deoxynucleosides and triphosphate. In CD4 + myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the P α -O 5' bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.

    • Organizational Affiliation: 
    • Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.

Macromolecule Content 

  • Total Structure Weight: 991.41 kDa 
  • Atom Count: 62,976 
  • Modeled Residue Count: 7,666 
  • Deposited Residue Count: 8,320 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
520Homo sapiensMutation(s): 1 
Gene Names: SAMHD1, MOP5
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CZF
(Subject of Investigation/LOI)

Query on CZF


Download:Ideal Coordinates CCD File
AC [auth H]
BB [auth E]
DA [auth B]
EE [auth O]
GD [auth L]
AC [auth H],
BB [auth E],
DA [auth B],
EE [auth O],
GD [auth L],
JB [auth F],
KC [auth J],
MA [auth C],
ME [auth P],
ND [auth M],
OA [auth C],
QC [auth J],
SB [auth G],
V [auth A],
VD [auth N],
ZC [auth K]
[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
C10 H15 N4 O15 P3
CAEFEWVYEZABLA-UUOKFMHZSA-N
XG4
(Subject of Investigation/LOI)

Query on XG4


Download:Ideal Coordinates CCD File
AB [auth E]
CA [auth B]
DB [auth E]
DE [auth O]
FA [auth B]
AB [auth E],
CA [auth B],
DB [auth E],
DE [auth O],
FA [auth B],
FD [auth L],
GA [auth C],
GC [auth I],
GE [auth P],
IB [auth F],
IC [auth I],
JC [auth I],
LA [auth C],
LB [auth F],
LE [auth P],
MB [auth G],
MD [auth M],
PA [auth D],
PC [auth J],
PD [auth M],
RB [auth G],
SC [auth J],
TC [auth K],
U [auth A],
UA [auth D],
UB [auth H],
UD [auth N],
X [auth A],
XD [auth N],
YC [auth K],
YD [auth O],
ZB [auth H]
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
C10 H17 N6 O12 P3
DWGAAFQEGIMTIA-KVQBGUIXSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
AD [auth K]
BC [auth H]
CB [auth E]
EA [auth B]
FE [auth O]
AD [auth K],
BC [auth H],
CB [auth E],
EA [auth B],
FE [auth O],
HC [auth I],
HD [auth L],
KB [auth F],
NA [auth C],
OD [auth M],
RC [auth J],
TB [auth G],
VA [auth D],
W [auth A],
WD [auth N]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
(Subject of Investigation/LOI)

Query on FE


Download:Ideal Coordinates CCD File
BD [auth L]
CC [auth I]
EB [auth F]
HA [auth C]
HE [auth P]
BD [auth L],
CC [auth I],
EB [auth F],
HA [auth C],
HE [auth P],
ID [auth M],
LC [auth J],
NB [auth G],
Q [auth A],
QA [auth D],
QD [auth N],
UC [auth K],
VB [auth H],
WA [auth E],
Y [auth B],
ZD [auth O]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG


Download:Ideal Coordinates CCD File
AA [auth B]
AE [auth O]
BA [auth B]
BE [auth O]
CD [auth L]
AA [auth B],
AE [auth O],
BA [auth B],
BE [auth O],
CD [auth L],
CE [auth O],
DC [auth I],
DD [auth L],
EC [auth I],
ED [auth L],
FB [auth F],
FC [auth I],
GB [auth F],
HB [auth F],
IA [auth C],
IE [auth P],
JA [auth C],
JD [auth M],
JE [auth P],
KA [auth C],
KD [auth M],
KE [auth P],
LD [auth M],
MC [auth J],
NC [auth J],
OB [auth G],
OC [auth J],
PB [auth G],
QB [auth G],
R [auth A],
RA [auth D],
RD [auth N],
S [auth A],
SA [auth D],
SD [auth N],
T [auth A],
TA [auth D],
TD [auth N],
VC [auth K],
WB [auth H],
WC [auth K],
XA [auth E],
XB [auth H],
XC [auth K],
YA [auth E],
YB [auth H],
Z [auth B],
ZA [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.782α = 90
b = 172.897β = 95.2
c = 275.886γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom108014/Z/15/Z
Wellcome TrustUnited KingdomFC001178
Medical Research Council (MRC, United Kingdom)United KingdomFC001178
Cancer Research UKUnited KingdomFC001178

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary