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- PDB-7a5y: Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-... -

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Basic information

Entry
Database: PDB / ID: 7a5y
TitleCrystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / triphosphohydrolase / metallo-enzyme / binuclear / HD
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 / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / 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 / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / 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 / RNA nuclease activity / somatic hypermutation of immunoglobulin genes / 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
: / 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsMorris, E.R. / Kunzelmann, S. / Caswell, S.J. / Purkiss, A. / Taylor, I.A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust108014/Z/15/Z United Kingdom
Wellcome TrustFC001178 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001178 United Kingdom
Cancer Research UKFC001178 United Kingdom
CitationJournal: Biochemistry / Year: 2021
Title: Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R p - and S p -dNTP alpha S Diastereomers.
Authors: Morris, E.R. / Kunzelmann, S. / Caswell, S.J. / Purkiss, A.G. / Kelly, G. / Taylor, I.A.
History
DepositionAug 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Refinement description
Category: citation / citation_author / pdbx_refine_tls_group
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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
E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,72264
Polymers481,1348
Non-polymers13,58856
Water6,179343
1
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)247,36132
Polymers240,5674
Non-polymers6,79428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19420 Å2
ΔGint-176 kcal/mol
Surface area64870 Å2
MethodPISA
2
E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,36132
Polymers240,5674
Non-polymers6,79428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19610 Å2
ΔGint-178 kcal/mol
Surface area64680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.193, 181.263, 286.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPROAA114 - 5818 - 475
21THRTHRPROPROBB114 - 5818 - 475
12ASPASPPROPROAA113 - 5817 - 475
22ASPASPPROPROCC113 - 5817 - 475
13THRTHRTHRTHRAA114 - 5798 - 473
23THRTHRTHRTHRDD114 - 5798 - 473
14THRTHRPROPROAA114 - 5818 - 475
24THRTHRPROPROEE114 - 5818 - 475
15ASPASPPROPROAA113 - 5817 - 475
25ASPASPPROPROFF113 - 5817 - 475
16ASPASPPROPROAA113 - 5817 - 475
26ASPASPPROPROGG113 - 5817 - 475
17THRTHRPROPROAA114 - 5818 - 475
27THRTHRPROPROHH114 - 5818 - 475
18THRTHRGLNGLNBB114 - 5828 - 476
28THRTHRGLNGLNCC114 - 5828 - 476
19THRTHRPHEPHEBB114 - 5788 - 472
29THRTHRPHEPHEDD114 - 5788 - 472
110THRTHRGLNGLNBB114 - 5828 - 476
210THRTHRGLNGLNEE114 - 5828 - 476
111THRTHRPROPROBB114 - 5818 - 475
211THRTHRPROPROFF114 - 5818 - 475
112THRTHRGLNGLNBB114 - 5828 - 476
212THRTHRGLNGLNGG114 - 5828 - 476
113THRTHRPROPROBB114 - 5818 - 475
213THRTHRPROPROHH114 - 5818 - 475
114THRTHRTHRTHRCC114 - 5798 - 473
214THRTHRTHRTHRDD114 - 5798 - 473
115THRTHRGLNGLNCC114 - 5828 - 476
215THRTHRGLNGLNEE114 - 5828 - 476
116ASPASPPROPROCC113 - 5817 - 475
216ASPASPPROPROFF113 - 5817 - 475
117ASPASPPROPROCC113 - 5817 - 475
217ASPASPPROPROGG113 - 5817 - 475
118THRTHRPROPROCC114 - 5818 - 475
218THRTHRPROPROHH114 - 5818 - 475
119THRTHRTHRTHRDD114 - 5798 - 473
219THRTHRTHRTHREE114 - 5798 - 473
120THRTHRTHRTHRDD114 - 5798 - 473
220THRTHRTHRTHRFF114 - 5798 - 473
121THRTHRPHEPHEDD114 - 5788 - 472
221THRTHRPHEPHEGG114 - 5788 - 472
122THRTHRTHRTHRDD114 - 5798 - 473
222THRTHRTHRTHRHH114 - 5798 - 473
123THRTHRPROPROEE114 - 5818 - 475
223THRTHRPROPROFF114 - 5818 - 475
124THRTHRPROPROEE114 - 5818 - 475
224THRTHRPROPROGG114 - 5818 - 475
125THRTHRPROPROEE114 - 5818 - 475
225THRTHRPROPROHH114 - 5818 - 475
126ASPASPLYSLYSFF113 - 5807 - 474
226ASPASPLYSLYSGG113 - 5807 - 474
127THRTHRPROPROFF114 - 5818 - 475
227THRTHRPROPROHH114 - 5818 - 475
128THRTHRPROPROGG114 - 5818 - 475
228THRTHRPROPROHH114 - 5818 - 475

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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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: 60141.738 Da / Num. of mol.: 8 / Mutation: H215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-T8T / 2'-deoxyguanosine-5'-O-(1-thiotriphosphate)


Mass: 523.247 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.29→153.15 Å / Num. obs: 145900 / % possible obs: 92.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.7 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.11 / Rrim(I) all: 0.287 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.29-2.456.51.5361.672950.5460.6461.66857.6
6.92-153.26.40.08316.172940.9950.0350.09199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.9 Å153.15 Å
Translation6.9 Å153.15 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TX0

6tx0


Resolution: 2.29→153.15 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.905 / SU B: 21.265 / SU ML: 0.229 / SU R Cruickshank DPI: 0.7188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.719 / ESU R Free: 0.286
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 7326 5 %RANDOM
Rwork0.2101 ---
obs0.2117 138594 77.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.65 Å2 / Biso mean: 37.524 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-0 Å2
2--0.67 Å2-0 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 2.29→153.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29346 0 776 343 30465
Biso mean--24.19 22.66 -
Num. residues----3650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01930831
X-RAY DIFFRACTIONr_bond_other_d0.0020.0227741
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.95341878
X-RAY DIFFRACTIONr_angle_other_deg1.0832.98864291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97353624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68123.8511493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.878155149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.17715199
X-RAY DIFFRACTIONr_chiral_restr0.110.24486
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02133850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026366
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A302840.05
12B302840.05
21A304280.05
22C304280.05
31A304240.05
32D304240.05
41A305260.05
42E305260.05
51A303140.05
52F303140.05
61A303300.05
62G303300.05
71A302260.05
72H302260.05
81B301100.05
82C301100.05
91B301180.05
92D301180.05
101B302380.05
102E302380.05
111B302760.05
112F302760.05
121B301560.05
122G301560.05
131B303240.05
132H303240.05
141C302060.05
142D302060.05
151C306620.05
152E306620.05
161C303520.05
162F303520.05
171C306540.05
172G306540.05
181C302160.05
182H302160.05
191D302880.05
192E302880.05
201D301960.05
202F301960.05
211D301220.05
212G301220.05
221D302320.04
222H302320.04
231E303180.05
232F303180.05
241E305420.04
242G305420.04
251E302340.04
252H302340.04
261F302500.05
262G302500.05
271F303360.05
272H303360.05
281G302400.04
282H302400.04
LS refinement shellResolution: 2.29→2.35 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.298 80 -
Rwork0.31 1653 -
obs--12.55 %
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)
11.17330.11710.04630.8205-0.06861.43710.00910.001-0.1597-0.02330.0114-0.18870.19980.2313-0.02050.13480.03260.00030.0379-0.00740.0593-16.073-5.592-114.064
21.4493-0.5282-0.28651.63390.22841.29310.02650.0031-0.10980.1292-0.04260.3671-0.0022-0.23690.01610.0988-0.01410.0250.047-0.00260.0837-46.5432.123-99.539
31.10280.05280.04210.89210.15411.3248-0.02890.0810.1458-0.1071-0.03570.2374-0.1927-0.14430.06460.15610.0187-0.0430.023-0.00140.08-41.51635.116-123.428
41.2801-0.10660.19710.90920.0121.39020.00590.04990.10240.0972-0.0378-0.1591-0.12870.27960.03190.1336-0.0383-0.03120.05860.01480.0353-11.36135.01-106.345
51.3393-0.264-0.12760.76860.09411.49390.02480.0566-0.13590.02740.00210.14360.215-0.2853-0.0270.1464-0.0504-0.01030.05730.00670.0349-22.61-4.447-33.522
61.4830.4558-0.22251.2281-0.27141.52260.03020.0093-0.0493-0.1297-0.034-0.31240.09190.31230.00380.10980.02670.03340.0667-0.00280.08538.0562.406-48.577
71.2468-0.11810.0340.8964-0.17241.0068-0.0057-0.12320.20780.1266-0.0125-0.2529-0.16150.14710.01810.1693-0.023-0.05360.0412-0.03290.13082.99336.603-26.393
81.28420.23480.12881.32330.14351.32160.0356-0.01710.0814-0.1017-0.06190.1787-0.0821-0.2870.02630.09870.0294-0.02260.066-0.00570.039-27.17335.325-43.398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 581
2X-RAY DIFFRACTION1A701 - 704
3X-RAY DIFFRACTION1B701 - 702
4X-RAY DIFFRACTION1C701
5X-RAY DIFFRACTION2B114 - 582
6X-RAY DIFFRACTION2A705 - 706
7X-RAY DIFFRACTION2B703 - 706
8X-RAY DIFFRACTION2D701
9X-RAY DIFFRACTION3C113 - 582
10X-RAY DIFFRACTION3A707 - 708
11X-RAY DIFFRACTION3C702 - 705
12X-RAY DIFFRACTION3D702
13X-RAY DIFFRACTION4D114 - 579
14X-RAY DIFFRACTION4B707 - 708
15X-RAY DIFFRACTION4C706
16X-RAY DIFFRACTION4D703 - 706
17X-RAY DIFFRACTION5E114 - 582
18X-RAY DIFFRACTION5E701 - 705
19X-RAY DIFFRACTION5F701 - 702
20X-RAY DIFFRACTION6F113 - 581
21X-RAY DIFFRACTION6E706
22X-RAY DIFFRACTION6F703 - 707
23X-RAY DIFFRACTION6H701
24X-RAY DIFFRACTION7G113 - 588
25X-RAY DIFFRACTION7E707 - 708
26X-RAY DIFFRACTION7G701 - 704
27X-RAY DIFFRACTION7H702
28X-RAY DIFFRACTION8H114 - 581
29X-RAY DIFFRACTION8F708 - 709
30X-RAY DIFFRACTION8G705
31X-RAY DIFFRACTION8H703 - 706

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