8QXN | pdb_00008qxn

Cryo-EM structure of tetrameric human SAMHD1 State IV - Depleted relaxed

PDB DOI: https://doi.org/10.2210/pdb8QXN/pdb
EM Map EMD-18733: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-24 Released: 2024-05-15
Deposition Author(s): Acton, O.J., Sheppard, D., Rosenthal, P.B., Taylor, I.A.
Funding Organization(s): Cancer Research UK, Medical Research Council (MRC, United Kingdom), Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis.

Acton, O.J., Sheppard, D., Kunzelmann, S., Caswell, S.J., Nans, A., Burgess, A.J.O., Kelly, G., Morris, E.R., Rosenthal, P.B., Taylor, I.A.

(2024) Nat Commun 15: 3775-3775

PubMed: 38710701 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-48237-w
Primary Citation Related Structures:
8QXJ, 8QXK, 8QXL, 8QXM, 8QXN, 8QXO

PubMed Abstract:
SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 294.63 kDa
Atom Count: 14,461
Modeled Residue Count: 1,760
Deposited Residue Count: 2,504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1	A, B, C, D	626	Homo sapiens	Mutation(s): 0 Gene Names: SAMHD1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y3Z3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain P [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain V [auth D] MOL2 format, chain P [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain V [auth D] mmCIF format, chain P [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], P [auth C], V [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain V [auth D]
DTP Query on DTP Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain S [auth D] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain S [auth D] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], O [auth B], S [auth D]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain S [auth D]
DCP (Subject of Investigation/LOI) Query on DCP Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain N [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain N [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain N [auth B]	N [auth B], Z [auth D]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₃ P₃ RGWHQCVHVJXOKC-SHYZEUOFSA-N		Interactions Focus chain N [auth B] Focus chain Z [auth D] Interactions & Density Focus chain N [auth B] Focus chain Z [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], Q [auth C], W [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A] L [auth B] M [auth B] R [auth C] T [auth D] G [auth A], L [auth B], M [auth B], R [auth C], T [auth D], U [auth D], X [auth D], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	CC2029.CC2106
Medical Research Council (MRC, United Kingdom)	United Kingdom	CC2029.CC2106
Wellcome Trust	United Kingdom	CC2029.CC2106