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

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Basic information

Entry
Database: PDB / ID: 6brg
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. / Sterile alpha motif. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,2848
Polymers310,1874
Non-polymers974
Water95553
1
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5712
Polymers77,5471
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,1424
Polymers155,0942
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-34 kcal/mol
Surface area45130 Å2
MethodPISA
3
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5712
Polymers77,5471
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5712
Polymers77,5471
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,1424
Polymers155,0942
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-35 kcal/mol
Surface area45020 Å2
MethodPISA
6
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5712
Polymers77,5471
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.582, 109.919, 162.089
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 72 - 624 / Label seq-ID: 86 - 638

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1


Mass: 77546.781 Da / Num. of mol.: 4
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.92 %
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-E / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 34596 / % possible obs: 98.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.4
Reflection shellResolution: 3.5→3.56 Å

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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: 0.89 / Cor.coef. Fo:Fc free: 0.856 / SU B: 100.187 / SU ML: 0.663 / Cross valid method: THROUGHOUT / ESU R Free: 0.706
RfactorNum. reflection% reflectionSelection details
Rfree0.27769 1725 5 %RANDOM
Rwork0.24351 ---
obs0.24528 32885 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 89.157 Å2
Baniso -1Baniso -2Baniso -3
1--3.06 Å20 Å22.3 Å2
2---5.81 Å20 Å2
3---6.53 Å2
Refinement stepCycle: 1 / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16514 0 4 53 16571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916878
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.95622689
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3351976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64723.531875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.415153141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61515139
X-RAY DIFFRACTIONr_chiral_restr0.0630.22400
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112787
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_it2.5254.8477976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2957.269928
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2815.2168902
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.95546.00971111
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A13380.04
12B13380.04
21A13480.04
22C13480.04
31A13520.03
32D13520.03
41B13540.04
42C13540.04
51B13400.04
52D13400.04
61C13560.04
62D13560.04
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 124 -
Rwork0.321 2352 -
obs--98.53 %
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)
110.1597-0.99460.640311.41920.85674.08190.24530.7401-0.6664-0.4737-0.11210.15920.76670.2921-0.13320.7090.01690.08760.2181-0.10770.088731.3551-21.987515.3474
22.878-0.3031-1.24342.21340.93764.62370.0155-0.70210.03880.3526-0.0279-0.55870.1260.60610.01240.13250.0216-0.07350.230.04680.159435.3776-3.994753.5758
38.0664-0.2389-3.71764.2327-0.42027.4372-0.0164-0.00360.09260.2369-0.05460.2094-0.1734-0.67980.07090.5787-0.0511-0.07210.4768-0.20730.27458.386726.474680.596
41.91820.4777-0.27913.1631.13863.1675-0.02310.01360.5839-0.3038-0.01810.3034-0.2048-0.48350.04120.04740.049-0.05060.1535-0.05740.23285.77359.791442.1029
56.7538-0.7778-1.797611.2372.56387.53030.1348-0.06211.0898-0.00160.08780.4018-0.7379-0.4173-0.22260.37890.30180.00230.3779-0.1391.093718.17366.389840.4321
64.884-0.6764-0.35882.76120.32721.4319-0.2285-0.87040.17110.6387-0.00090.18140.03710.15020.22940.18930.0402-0.02140.1913-0.06530.129150.38339.139443.256
78.336-0.7169-1.4439.61221.921512.59060.75021.0775-0.7445-0.2547-0.4451-0.61951.08491.1881-0.30510.51160.3457-0.01810.434-0.05470.541569.5473.707715.8348
82.5663-0.9032-0.10693.96590.32561.8015-0.25220.38430.0906-0.49320.19780.69040.1368-0.25360.05440.1577-0.1129-0.12050.12750.07990.146836.315630.148112.986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 146
2X-RAY DIFFRACTION2A147 - 496
3X-RAY DIFFRACTION2A800
4X-RAY DIFFRACTION2A911
5X-RAY DIFFRACTION2A497 - 624
6X-RAY DIFFRACTION3B72 - 146
7X-RAY DIFFRACTION4B147 - 496
8X-RAY DIFFRACTION4D800
9X-RAY DIFFRACTION4D904
10X-RAY DIFFRACTION4B497 - 624
11X-RAY DIFFRACTION5C72 - 146
12X-RAY DIFFRACTION6C147 - 496
13X-RAY DIFFRACTION6C800
14X-RAY DIFFRACTION6C906
15X-RAY DIFFRACTION6C497 - 624
16X-RAY DIFFRACTION7D72 - 146
17X-RAY DIFFRACTION8D147 - 496
18X-RAY DIFFRACTION8B800
19X-RAY DIFFRACTION8B909
20X-RAY DIFFRACTION8D497 - 624

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