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- PDB-8d9j: SAMHD1-DNA complex -

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Basic information

Entry
Database: PDB / ID: 8d9j
TitleSAMHD1-DNA complex
Components
  • DNA (5'-D(*CP*AP*AP*TP*G)-3')
  • Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE/DNA / DNA complex / catalytic domain / dNTP hydrolysis / ANTIVIRAL PROTEIN / HYDROLASE-DNA complex
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 / 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
: / 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
: / DNA / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsHollis, T.J. / Batalis, S.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108827A United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM095440 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32-AI007401 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA012197-47 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Protein oxidation increases SAMHD1 binding ssDNA via its regulatory site.
Authors: Simermeyer, T.L. / Batalis, S. / Rogers, L.C. / Zalesak, O.J. / Hollis, T.
History
DepositionJun 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: DNA (5'-D(*CP*AP*AP*TP*G)-3')
G: DNA (5'-D(*CP*AP*AP*TP*G)-3')
H: DNA (5'-D(*CP*AP*AP*TP*G)-3')
I: DNA (5'-D(*CP*AP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,62116
Polymers295,2388
Non-polymers3848
Water3,513195
1
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: DNA (5'-D(*CP*AP*AP*TP*G)-3')
I: DNA (5'-D(*CP*AP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8118
Polymers147,6194
Non-polymers1924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: DNA (5'-D(*CP*AP*AP*TP*G)-3')
G: DNA (5'-D(*CP*AP*AP*TP*G)-3')
H: DNA (5'-D(*CP*AP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3159
Polymers149,1235
Non-polymers1924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.430, 179.678, 79.891
Angle α, β, γ (deg.)90.000, 109.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM domain and HD domain-containing protein 1 / hSAMHD1


Mass: 72305.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3)
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
#2: DNA chain
DNA (5'-D(*CP*AP*AP*TP*G)-3')


Mass: 1504.037 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl pH 7.5, 150 mM CaCl2, 20% PEG 3350, and 4% 2-methyl-2,4-pentanediol (MPD)
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 47336 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 55.39 Å2 / CC1/2: 0.98 / Net I/σ(I): 8.1
Reflection shellResolution: 2.85→2.93 Å / Redundancy: 6.5 % / Num. unique obs: 3958 / CC1/2: 0.55 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3u1n

3u1n


Resolution: 2.82→39.05 Å / SU ML: 0.3321 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2421 2328 4.97 %
Rwork0.1822 44498 -
obs0.1851 46826 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.36 Å2
Refinement stepCycle: LAST / Resolution: 2.82→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14282 186 8 195 14671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002414825
X-RAY DIFFRACTIONf_angle_d0.510920067
X-RAY DIFFRACTIONf_chiral_restr0.04192154
X-RAY DIFFRACTIONf_plane_restr0.00412569
X-RAY DIFFRACTIONf_dihedral_angle_d8.15822020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.880.30021270.26292188X-RAY DIFFRACTION83.42
2.88-2.940.31091450.25962592X-RAY DIFFRACTION96.61
2.94-3.010.31461500.252644X-RAY DIFFRACTION97.69
3.01-3.090.36771200.26562602X-RAY DIFFRACTION97.7
3.09-3.170.30021440.24752606X-RAY DIFFRACTION97
3.17-3.260.33461380.21772597X-RAY DIFFRACTION97.54
3.26-3.370.27621350.2092645X-RAY DIFFRACTION98.2
3.37-3.490.26191490.19972643X-RAY DIFFRACTION98.83
3.49-3.630.29651480.19212662X-RAY DIFFRACTION98.98
3.63-3.80.24771350.18182669X-RAY DIFFRACTION98.77
3.8-40.20781530.16082605X-RAY DIFFRACTION97.66
4-4.250.20141290.15242611X-RAY DIFFRACTION97.3
4.25-4.570.19571270.14582685X-RAY DIFFRACTION99.47
4.57-5.030.18531390.14772709X-RAY DIFFRACTION99.3
5.03-5.760.2381240.17112676X-RAY DIFFRACTION99.4
5.76-7.250.25651290.19132677X-RAY DIFFRACTION98.84
7.25-39.050.19531360.15382687X-RAY DIFFRACTION97.68

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