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Open data
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Basic information
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Title | Cryo-EM structure of tetrameric human SAMHD1 with dApNHpp | ||||||||||||
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![]() | TRIPHOSPHOHYDROLASE / METALLO-ENZYME / BINUCLEAR / HD / HYDROLASE | ||||||||||||
Function / homology | ![]() Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / deoxyribonucleotide catabolic process / dGTP catabolic process ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / deoxyribonucleotide catabolic process / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | ||||||||||||
![]() | Acton OJ / Sheppard D / Rosenthal PB / Taylor IA | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis. Authors: Oliver J Acton / Devon Sheppard / Simone Kunzelmann / Sarah J Caswell / Andrea Nans / Ailidh J O Burgess / Geoff Kelly / Elizabeth R Morris / Peter B Rosenthal / Ian A Taylor / ![]() 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- ...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. | ||||||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.8 KB | Display | ![]() |
Images | ![]() | 73.7 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 216.6 MB 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qxjMC ![]() 8qxkC ![]() 8qxlC ![]() 8qxmC ![]() 8qxnC ![]() 8qxoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
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-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : homotetramer of SAMHD1
Entire | Name: homotetramer of SAMHD1 |
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Components |
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-Supramolecule #1: homotetramer of SAMHD1
Supramolecule | Name: homotetramer of SAMHD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Macromolecule | Name: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 72.305414 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MQRADSEQPS KRPRCDDSPR TPSNTPSAEA DWSPGLELHP DYKTWGPEQV CSFLRRGGFE EPVLLKNIRE NEITGALLPC LDESRFENL GVSSLGERKK LLSYIQRLVQ IHVDTMKVIN DPIHGHIELH PLLVRIIDTP QFQRLRYIKQ LGGGYYVFPG A SHNRFEHS ...String: MQRADSEQPS KRPRCDDSPR TPSNTPSAEA DWSPGLELHP DYKTWGPEQV CSFLRRGGFE EPVLLKNIRE NEITGALLPC LDESRFENL GVSSLGERKK LLSYIQRLVQ IHVDTMKVIN DPIHGHIELH PLLVRIIDTP QFQRLRYIKQ LGGGYYVFPG A SHNRFEHS LGVGYLAGCL VHALGEKQPE LQISERDVLC VQIAGLCHDL GHGPFSHMFD GRFIPLARPE VKWTHEQGSV MM FEHLINS NGIKPVMEQY GLIPEEDICF IKEQIVGPLE SPVEDSLWPY KGRPENKSFL YEIVSNKRNG IDVDKWDYFA RDC HHLGIQ NNFDYKRFIK FARVCEVDNE LRICARDKEV GNLYDMFHTR NSLHRRAYQH KVGNIIDTMI TDAFLKADDY IEIT GAGGK KYRISTAIDD MEAYTKLTDN IFLEILYSTD PKLKDAREIL KQIEYRNLFK YVGETQPTGQ IKIKREDYES LPKEV ASAK PKVLLDVKLK AEDFIVDVIN MDYGMQEKNP IDHVSFYCKT APNRAIRITK NQVSQLLPEK FAEQLIRVYC KKVDRK SLY AARQYFVQWC ADRNFTKPQD GDVIAPLITP QKKEWNDSTS VQNPTRLREA SKSRVQLFKD DPM UniProtKB: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 |
-Macromolecule #2: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]a...
Macromolecule | Name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine type: ligand / ID: 2 / Number of copies: 8 / Formula: DZ4 |
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Molecular weight | Theoretical: 490.197 Da |
Chemical component information | ![]() ChemComp-DZ4: |
-Macromolecule #3: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 214 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 48.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: LAB6 |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-8qxj: |