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- EMDB-41175: ssRNA bound SAMHD1 T open -

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Basic information

Entry
Database: EMDB / ID: EMD-41175
TitlessRNA bound SAMHD1 T open
Map dataT*-open form
Sample
  • Complex: ssRNA bound SAMHD1 T open
    • Complex: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
      • Protein or peptide: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
    • Complex: RNA
      • RNA: RNA (5'-R(P*CP*CP*GP*GP*CP*C)-3')
      • RNA: RNA (5'-R(P*CP*CP*GP*AP*CP*C)-3')
  • Ligand: FE (III) ION
KeywordsDeoxynucleoside triphosphate triphosphohydrolase / HYDROLASE
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / 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 / single-stranded DNA binding / site of double-strand break / defense response to virus / protein homotetramerization / 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
: / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human) / Virus-associated RNAs
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsSung M / Huynh K / Han S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Guanine-containing ssDNA and RNA induce dimeric and tetrameric structural forms of SAMHD1.
Authors: Benjamin Orris / Min Woo Sung / Shridhar Bhat / Yingrong Xu / Kevin W Huynh / Seungil Han / Darren C Johnson / Benedikt Bosbach / David J Shields / James T Stivers /
Abstract: The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates ...The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates with stalled DNA replication forks, DNA repair foci, ssRNA and telomeres. The above functions require nucleic acid binding by SAMHD1, which may be modulated by its oligomeric state. Here we establish in cryo-EM and biochemical studies that the guanine-specific A1 activator site of each SAMHD1 monomer is used to target the enzyme to guanine nucleotides within single-stranded (ss) DNA and RNA. Remarkably, nucleic acid strands containing a single guanine base induce dimeric SAMHD1, while two or more guanines with ∼20 nucleotide spacing induce a tetrameric form. A cryo-EM structure of ssRNA-bound tetrameric SAMHD1 shows how ssRNA strands bridge two SAMHD1 dimers and stabilize the structure. This ssRNA-bound tetramer is inactive with respect to dNTPase and RNase activity.
History
DepositionJul 5, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41175.png

Downloads & links

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Map

FileDownload / File: emd_41175.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT*-open form
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 220 pix.
= 263.89 Å		1.2 Å/pix.
x 220 pix.
= 263.89 Å		1.2 Å/pix.
x 220 pix.
= 263.89 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1995 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-3.43161 - 4.434322
Average (Standard dev.)0.000016669814 (±0.06913633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 263.88998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41175_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: T*-open form-even

Fileemd_41175_half_map_1.map
AnnotationT*-open form-even
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: T*-open form-odd

Fileemd_41175_half_map_2.map
AnnotationT*-open form-odd
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Sample components

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Entire : ssRNA bound SAMHD1 T open

EntireName: ssRNA bound SAMHD1 T open
Components
  • Complex: ssRNA bound SAMHD1 T open
    • Complex: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
      • Protein or peptide: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
    • Complex: RNA
      • RNA: RNA (5'-R(P*CP*CP*GP*GP*CP*C)-3')
      • RNA: RNA (5'-R(P*CP*CP*GP*AP*CP*C)-3')
  • Ligand: FE (III) ION

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Supramolecule #1: ssRNA bound SAMHD1 T open

SupramoleculeName: ssRNA bound SAMHD1 T open / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

SupramoleculeName: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

MacromoleculeName: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.305414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: RNA (5'-R(P*CP*CP*GP*GP*CP*C)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*GP*GP*CP*C)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Virus-associated RNAs
Molecular weightTheoretical: 1.866181 KDa
SequenceString:
CCGGCC

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Macromolecule #3: RNA (5'-R(P*CP*CP*GP*AP*CP*C)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*GP*AP*CP*C)-3') / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Virus-associated RNAs
Molecular weightTheoretical: 1.850181 KDa
SequenceString:
CCGACC

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Macromolecule #4: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135791
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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