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- PDB-9que: Structure of human MTH1 in complex with 8DG by continuous serial ... -

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Basic information

Entry
Database: PDB / ID: 9que
TitleStructure of human MTH1 in complex with 8DG by continuous serial electron diffraction (SerialED)
ComponentsOxidized purine nucleoside triphosphate hydrolase
KeywordsHYDROLASE / serial electron diffraction / SerialED / MTH1 / 8DG
Function / homology
Function and homology information


2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.66 Å
AuthorsHofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Scaletti Hutchinson, E. / Stenmark, P. / Di Palma, M. / Williams, L. / Worral, J. ...Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Scaletti Hutchinson, E. / Stenmark, P. / Di Palma, M. / Williams, L. / Worral, J. / Steiner, R. / Xu, H. / Zou, X.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Continuous Serial Electron Diffraction for High Quality Protein Structures
Authors: Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Williams, L. / Worrall, J. / Steiner, R. / Xu, H. / Zou, X.
History
DepositionApr 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidized purine nucleoside triphosphate hydrolase
B: Oxidized purine nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9388
Polymers36,5072
Non-polymers1,4316
Water2,540141
1
A: Oxidized purine nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9694
Polymers18,2541
Non-polymers7153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidized purine nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9694
Polymers18,2541
Non-polymers7153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.340, 67.550, 80.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Oxidized purine nucleoside triphosphate hydrolase / 2-hydroxy-dATP diphosphatase / 7 / 8-dihydro-8-oxoguanine triphosphatase / 8-oxo-dGTPase / ...2-hydroxy-dATP diphosphatase / 7 / 8-dihydro-8-oxoguanine triphosphatase / 8-oxo-dGTPase / Methylated purine nucleoside triphosphate hydrolase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18253.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P36639, 2-hydroxy-dATP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: 7,8-dihydro-8-oxoguanine triphosphatase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.0182 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 4
Details: Crystals were produced by adding 1 part of precipitant mix (30% PEG-6k, 0.16 M Li2SO4, 0.1 M sodium acetate, pH 4) to 1 part of protein solution (14 mg/mL)
Buffer component
IDConc.NameFormulaBuffer-ID
130 %PEG-6k1
20.16 MLithium sulfateLi2SO41
30.1 Msodium acetateNaAc1
SpecimenConc.: 14 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE
Details: Manual blotting at room temperature with ambient humidity

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 98 K / Temperature (min): 78 K
Image recordingElectron dose: 5.63 e/Å2 / Film or detector model: FEI CETA (4k x 4k)
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
3.91-25.7311100100.21299318.42
1.66-1.712155.5100.21152943.28
EM diffraction statsFourier space coverage: 99.8 % / High resolution: 1.66 Å / Num. of intensities measured: 3882602 / Num. of structure factors: 38744 / Phase error rejection criteria: 0 / Rmerge: 13.6
ReflectionBiso Wilson estimate: 22.78 Å2

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Processing

EM software
IDNameCategory
12PHENIX3D reconstruction
13PHENIXmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 59.34 Å / B: 67.55 Å / C: 80.11 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 1.66 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 30.11 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: maximum-likelihood
Atomic model buildingPDB-ID: 3ZR1

3zr1


Accession code: 3ZR1 / Source name: PDB / Type: experimental model
RefinementResolution: 1.66→25.73 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1856 5 %Random selection
Rwork0.2051 35264 --
obs0.2074 37120 96.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.01042711
ELECTRON CRYSTALLOGRAPHYf_angle_d0.94723686
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.059375
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0079467
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d16.7298365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.710.4238750.37641529ELECTRON CRYSTALLOGRAPHY55.48
1.71-1.760.36971490.34732702ELECTRON CRYSTALLOGRAPHY97.8
1.76-1.810.34651380.30512776ELECTRON CRYSTALLOGRAPHY99.28
1.81-1.880.33171550.28872773ELECTRON CRYSTALLOGRAPHY99.69
1.88-1.950.30751470.25762768ELECTRON CRYSTALLOGRAPHY99.9
1.95-2.040.28121410.23982802ELECTRON CRYSTALLOGRAPHY99.93
2.04-2.150.26681500.21352774ELECTRON CRYSTALLOGRAPHY100
2.15-2.290.24531490.19582805ELECTRON CRYSTALLOGRAPHY99.93
2.29-2.460.24691440.19842795ELECTRON CRYSTALLOGRAPHY100
2.46-2.710.26251480.19252834ELECTRON CRYSTALLOGRAPHY99.97
2.71-3.10.2491510.20262850ELECTRON CRYSTALLOGRAPHY100
3.1-3.910.221500.17182863ELECTRON CRYSTALLOGRAPHY100
3.91-25.730.2231590.18242993ELECTRON CRYSTALLOGRAPHY100
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON CRYSTALLOGRAPHY

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)
12.86161070534-1.029833499260.7862424003113.069775720.4092125410.881485638934-0.01160550538-0.1741330330320.996135070713-0.0726061119322-0.05791008660390.01674411340070.0301430993148-0.2601756366580.04324284141380.170371632016-0.02467416928990.02182522858710.201692991948-0.08127320044530.40429784392433.993231428512.9730989954-7.61428122464
21.792452757660.1861334453650.5046896938621.91156769090.6294902485320.887713030590.0313726762244-0.5723931183821.096437565080.03684132495630.0989667972585-0.146034576689-0.05138607411510.02342371614240.1302774477220.1662143011230.01562248361640.0179213063370.289597396439-0.1842039299360.38815949911927.330584439913.0490056392-7.44135464928
34.336420189760.03345197282220.7285378670063.44087712054-1.938486612916.881485724260.291456063808-0.1733336288940.132799672673-0.39358218181-0.01745881900760.05960798246860.346680047077-0.00536240836455-0.09962571231160.186529761383-0.0402633458528-0.009205856178010.1326165391440.01126505505950.12027949758820.13806640523.85468515394-13.171180614
42.24058330819-0.157176691977-0.0473457029562.669373066430.828329478591.94194531313-0.0274815363487-0.06026652992730.158771248934-0.00714149558504-0.000281074039844-0.00985878078691-0.1508418959720.0006936363552230.09481397582960.1636317483430.0212413208504-0.009938460789950.1043762807150.01158900085840.135788479655-5.28317131405-11.1717929643-11.5750566157
52.285215790710.873774391466-0.04503744044452.60736266780.156705327020.4539388651580.0350943122332-0.134942670526-0.003739196412660.146729651356-0.000549834829271-0.01080855428310.0158219537132-0.012311924242-0.03262896690170.168804363560.00771764607528-0.01917411455190.08932730950840.002729815938540.1081065578423.11003203339-10.441901198-10.6435558493
Refinement TLS group

Refine-ID: ELECTRON CRYSTALLOGRAPHY

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 3 through 57 )BD3 - 571 - 55
22chain 'B' and (resid 58 through 128 )BD58 - 12856 - 126
33chain 'B' and (resid 129 through 156 )BD129 - 156127 - 154
44chain 'A' and (resid -1 through 57 )AA-1 - 571 - 59
55chain 'A' and (resid 58 through 156 )AA58 - 15660 - 158

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