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- PDB-6brk: The SAM domain of mouse SAMHD1 is critical for its activation and... -

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Basic information

Entry
Database: PDB / ID: 6brk
TitleThe SAM domain of mouse SAMHD1 is critical for its activation and regulation
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / dNTPase / Allosteric Regulation / Binding Sites / Mouse / Models / Molecular / Protein Conformation / Protein Multimerization
Function / homology
Function and homology information


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 / DNA strand resection involved in replication fork processing / deoxyribonucleotide 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 / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / dGTP catabolic process / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / double-strand break repair via homologous recombination / site of double-strand break / single-stranded DNA binding / protein homotetramerization / defense response to virus / nucleic acid binding / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBuzovetsky, O. / Tang, C. / Knecht, K.M. / Antonucci, J.M. / Wu, L. / Ji, X. / Xiong, Y.
CitationJournal: Nat Commun / Year: 2018
Title: The SAM domain of mouse SAMHD1 is critical for its activation and regulation.
Authors: Buzovetsky, O. / Tang, C. / Knecht, K.M. / Antonucci, J.M. / Wu, L. / Ji, X. / Xiong, Y.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1115
Polymers77,5651
Non-polymers1,5464
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules

A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,22110
Polymers155,1302
Non-polymers3,0928
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_435-x-1,-y-2,z1
Buried area9180 Å2
ΔGint-29 kcal/mol
Surface area43410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.755, 102.796, 145.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Deoxynucleoside triphosphate triphosphohydrolase SAMHD1


Mass: 77564.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Samhd1 / Production host: Escherichia coli (E. coli) / References: UniProt: F8WJE0, UniProt: Q60710*PLUS
#2: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.4 / Details: 100 mM SPG (Qiagen) buffer, pH 7.4, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9164 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9164 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 8255 / % possible obs: 98 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 19.6
Reflection shellResolution: 3.5→3.56 Å / Rmerge(I) obs: 0.71 / Num. unique all: 796

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AJA

5aja


Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.838 / SU B: 107.059 / SU ML: 0.671 / Cross valid method: THROUGHOUT / ESU R Free: 0.754
RfactorNum. reflection% reflectionSelection details
Rfree0.28523 392 4.8 %RANDOM
Rwork0.24208 ---
obs0.24403 7813 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 121.612 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---4.56 Å20 Å2
3---6.06 Å2
Refinement stepCycle: 1 / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 94 0 4225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194321
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9845831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3395494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40923.47219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.23315788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4991536
X-RAY DIFFRACTIONr_chiral_restr0.0930.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213233
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7995.3121994
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.867.9542482
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2345.7252324
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.53250.63418629
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.501→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 27 -
Rwork0.368 543 -
obs--95.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1166-1.35290.48613.6584-0.11624.8634-0.2155-0.14290.26070.26880.4853-0.2291-0.66310.5505-0.26980.50760.0383-0.090.5599-0.19280.7468-31.2523-61.6469164.6954
24.64640.96080.5874.9491-0.74081.27710.0366-0.15220.68560.11780.38591.3301-0.0698-0.6098-0.42250.30130.18910.20370.43570.22130.6762-57.9814-95.1412166.5086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 146
2X-RAY DIFFRACTION2A147 - 496
3X-RAY DIFFRACTION2A701 - 704
4X-RAY DIFFRACTION2A497 - 624

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