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- PDB-9quh: Structure of human MTH1 in complex with 8DG by MicroED using high... -

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Basic information

Entry
Database: PDB / ID: 9quh
TitleStructure of human MTH1 in complex with 8DG by MicroED using high electron fluence
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / serial electron diffraction / SerialED / MicroED / 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: 2.32 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

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Assembly

Deposited unit
A: 7,8-dihydro-8-oxoguanine triphosphatase
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8427
Polymers36,5072
Non-polymers1,3355
Water73941
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7772
Polymers18,2541
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0655
Polymers18,2541
Non-polymers8114
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 7,8-dihydro-8-oxoguanine triphosphatase / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / 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, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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
20.1 Msodium acetateNaAc1
30.16 Mlithium sulfateLi2SO41
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 / Calibrated defocus min: 0 nm / C2 aperture diameter: 20 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 98 K / Temperature (min): 78 K
Image recordingElectron dose: 0.37 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 (°)
4.43-29.351195.813.4350216.56
2.32-2.442143.513.4159545.09
EM diffraction statsFourier space coverage: 79.1 % / High resolution: 2.32 Å / Num. of intensities measured: 152619 / Num. of structure factors: 11420 / Phase error rejection criteria: 0 / Rmerge: 45.6
ReflectionBiso Wilson estimate: 30.2 Å2

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Processing

EM softwareName: PHENIX / Category: model 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: 2.32 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 29.72 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: Maximum-likelihood
Atomic model buildingPDB-ID: 3ZR1

3zr1


Accession code: 3ZR1 / Source name: PDB / Type: experimental model
RefinementResolution: 2.32→29.35 Å / SU ML: 0.3515 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 1049 5.02 %Ramdom selection
Rwork0.2036 19863 --
obs0.2065 20912 77.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0022665
ELECTRON CRYSTALLOGRAPHYf_angle_d0.48923623
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0426371
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0024459
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d16.2853357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.440.3914810.30461595ELECTRON CRYSTALLOGRAPHY43.52
2.44-2.590.3902950.29281777ELECTRON CRYSTALLOGRAPHY48.92
2.6-2.80.35781390.30242634ELECTRON CRYSTALLOGRAPHY72.52
2.8-3.080.33291740.25643335ELECTRON CRYSTALLOGRAPHY91.31
3.08-3.520.28951900.20873513ELECTRON CRYSTALLOGRAPHY96.18
3.52-4.430.21831850.15113507ELECTRON CRYSTALLOGRAPHY96.1
4.43-29.350.19131850.17333502ELECTRON CRYSTALLOGRAPHY95.79
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)
11.212036124980.06874326967070.1547620863650.1744276846480.3411832142620.668675499389-0.01128727648810.0115893521286-0.0238853644258-0.1468394239770.01523136550890.108052636835-0.0883508859516-0.0427911586341-0.380431099390.2623478779230.05919436382410.004482559528950.0929057727538-0.07967671594810.257200560673-4.3391578133-5.5109443823-11.5730425153
21.2585143639-0.577690306962-0.03755943454962.05003278096-0.6622810651664.232210976460.0138832680058-0.0408500089403-0.00791770947876-0.00313743826582-0.0824926712859-0.259327027867-0.0259006859373-0.384087518627-0.02773855165790.27509942033-0.0641923509099-0.0821290742760.1281870562740.02801479317390.183749871029-0.273676992893-19.0622251294-13.4475722153
33.08091136284-0.144354942971-0.6821189094163.823686550490.8817676283990.443146919563-0.298619834404-0.1353660274850.381899981175-0.0582236380332-0.041531519680.3980612252440.00825403540218-0.1618097404290.1036370903160.2870829632860.0199900734908-0.08591569789730.178109156527-0.03294516996270.162928694535-11.8057051795-9.4508300306-9.444306027
42.084694159721.148985184620.1103543614820.9826823442440.5343226265460.7397230202650.278736911131-0.5065539017160.004165824970910.254619227269-0.3294762112270.2150981936490.1887059796080.2054392790070.03285572016630.3216563830520.008389919429160.007390223308510.2493607017440.05588194956670.20649590607-2.36339987983-7.925322808-6.86689945745
50.8130176174960.412817928463-0.4073712247921.48977851636-0.4057399784480.683699015778-0.0512778685006-0.0599074839929-0.0679406410152-0.002229548958020.04590274685510.03183434367020.1924912284080.01782371814580.1096833737760.2003124068920.0242040460746-0.01742303364980.03506747721350.03310799285770.183521204736-1.41421257823-2.619896361-14.1137638116
63.60837969731-0.21803581327-0.6009954740481.370137713361.126268102891.727098964840.00191874227534-0.325795874691-0.3920584897560.1817137839970.2166825328870.02364571150210.31039702734-0.0653332731941-0.09183957166490.308556981678-0.02130792827660.03937804833010.1189738118770.02419014240750.166571524744-5.07901436195-23.2807692323-9.41803460217
70.757575868204-0.05471193726550.4819304638620.0338299192468-0.2351540304461.655804653040.0746973853444-0.107702772681-0.1011905104340.0773958053159-0.00161828376796-0.0171640935110.3427997887890.106969083613-0.1156496356360.360465476647-0.00473154243111-0.04868401002680.152837689798-0.01025567364910.0753549587488.74995973712-18.0007887045-14.3000564338
85.78742329627-0.696562415583-2.343159495193.325214460930.6869341762462.53974282729-0.165667586682-0.126871915302-0.3390712812420.679671523815-0.215434673564-0.001407925998220.1395980510170.0992365922950.3134281787410.226729950124-0.008155186313730.00445767781270.1742954443710.06341363573270.1698113555279.31632065722-10.6678560679-5.58520373658
92.825406228520.1691601914410.7877433580991.916930134031.203487887311.17445365307-0.189243670120.3131109048880.00747648407102-0.2524594338730.03753752871710.02785413540020.26698959876-0.201902046018-0.03268496973060.2442010277990.02731435577660.0201873370880.163249631145-0.01094716897950.07965110252647.28150091671-3.43318022753-17.9051107612
101.13501377182-0.1875086979290.2970843625461.224981859840.1567520156675.149004173840.16438088682-0.180857647188-0.09331706250850.3290303529-0.151990540965-0.1549289243890.102398004832-0.115915029824-0.2916875023840.215815568387-0.0585270316385-0.1120996219510.1174557248360.06912571124590.17329590095110.3090167733-1.09720656336-9.59704229836
111.03988443823-0.883099842321-0.9891264763614.456674435661.739511884463.65798266714-0.00899397121525-0.109757827792-0.0363671664279-0.5917495686730.0466623845397-0.204906342616-0.1430416134350.137006741922-0.6494911789340.1996462535010.00669534130529-0.0003066286996360.292712112018-0.1828474746360.3200193930833.21324167236.29208727863-11.2962565064
121.95026075649-2.22472909518-0.4070214181085.191768915162.002700572633.983451204620.150704580826-0.4869825824060.765301662212-0.259059960853-0.213107428535-0.0499632691644-0.0365293648187-0.196828058855-0.08880845877310.2319040933690.00976910222506-0.007164708024860.323463559361-0.1747997584730.4757491620528.107784519319.4797249642-7.93326714714
133.22627265504-3.19107280715-0.738008143416.415139483781.984413911821.78001986688-0.134636155622-0.15077255120.0847847200861-0.2846813035260.2499140415980.1269704593220.01846863671180.183705372214-0.1286199005830.172320117933-0.02465293303030.06325745678410.142272673491-0.01729202864370.36125439210839.65620787589.54797721006-6.11093995063
143.426535328280.6181261058960.6051917334373.202774058450.09416776269570.8733460101310.449841856055-0.57957203678-0.1856312265120.528507940662-0.115157996984-0.02898126848520.208025735554-0.0462952556526-0.1601543665960.208358319346-0.05859754494050.04936475919370.328747943214-0.08899563052050.32953796660630.3213827056.79078236403-5.83016156421
152.577612257590.06997747240330.8219259382672.797881580351.158481708258.097505359520.3127413376930.0563564906658-0.028787806496-0.275336350648-0.115206444664-0.0302850429703-0.489248285759-0.182933548776-0.01373345294930.1938449956710.07934931074640.0469486207880.133131646056-0.05697327545710.25742853390730.54049917475.11416629265-14.6815550862
161.25300814003-0.9794653421690.120566879530.770146133456-0.1129578447590.1125228537080.000663136545096-0.326714723660.585920974920.01029474644260.121363265511-0.491872746534-0.09720717458290.179740229698-0.2233761619360.2141581923260.02344238582110.0378963588760.398695782522-0.2848352479070.60578215195530.096956633321.9201735673-1.61340319773
170.148455707352-0.29274986387-0.1839036138652.212063710050.8336818081691.610455415660.0201185544698-0.007766338327510.0296895098872-0.103764827018-0.01853080527060.0460941302055-0.354699088609-0.0565773645788-0.1970652378940.3245379611410.01907222379270.00497461473820.206809046339-0.1824606170310.43708040395220.596099355619.0836367183-12.3933959116
185.2084484340.01761500853660.329060240755.72116068628-0.8132764198716.309453093780.199586094273-0.3829534016720.106769440897-0.0668547945403-0.02720627976050.204450661231-0.0336504500474-0.144306359878-0.2000099580070.1317181648760.0052560236224-0.01664973349050.154440588671-0.002317018223620.25971250430519.72149260195.67729489985-11.8562612427
Refinement TLS group

Refine-ID: ELECTRON CRYSTALLOGRAPHY

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 12 )AA3 - 121 - 10
22chain 'A' and (resid 13 through 34 )AA13 - 3411 - 32
33chain 'A' and (resid 35 through 57 )AA35 - 5733 - 55
44chain 'A' and (resid 58 through 74 )AA58 - 7456 - 72
55chain 'A' and (resid 75 through 88 )AA75 - 8873 - 86
66chain 'A' and (resid 89 through 107 )AA89 - 10787 - 105
77chain 'A' and (resid 108 through 119 )AA108 - 119106 - 117
88chain 'A' and (resid 120 through 132 )AA120 - 132118 - 130
99chain 'A' and (resid 133 through 143 )AA133 - 143131 - 141
1010chain 'A' and (resid 144 through 156 )AA144 - 156142 - 154
1111chain 'B' and (resid 2 through 12 )BC2 - 121 - 11
1212chain 'B' and (resid 13 through 33 )BC13 - 3312 - 32
1313chain 'B' and (resid 34 through 57 )BC34 - 5733 - 56
1414chain 'B' and (resid 58 through 74 )BC58 - 7457 - 73
1515chain 'B' and (resid 75 through 88 )BC75 - 8874 - 87
1616chain 'B' and (resid 89 through 110 )BC89 - 11088 - 109
1717chain 'B' and (resid 111 through 117 )BC111 - 117110 - 116
1818chain 'B' and (resid 118 through 156 )BC118 - 156117 - 155

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