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- PDB-9q0o: Cryo-EM structure of PPAT-NUDT5 complex bound to 6-benzylthioinos... -

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Basic information

Entry
Database: PDB / ID: 9q0o
TitleCryo-EM structure of PPAT-NUDT5 complex bound to 6-benzylthioinosine-5'-monophosphate (6-benzylTIMP)
Components
  • ADP-sugar pyrophosphatase
  • Amidophosphoribosyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Purine synthesis / phosphoribosyltransferase
Function / homology
Function and homology information


amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / 8-oxo-dGDP phosphatase / ADP-sugar pyrophosphatase activity / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / ADP-ribose diphosphatase activity ...amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / 8-oxo-dGDP phosphatase / ADP-sugar pyrophosphatase activity / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / ADP-ribose diphosphatase activity / D-ribose catabolic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 8-oxo-dGDP phosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 'de novo' AMP biosynthetic process / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / purine nucleotide biosynthetic process / GMP biosynthetic process / nucleotide metabolic process / 'de novo' IMP biosynthetic process / snoRNA binding / nucleotidyltransferase activity / 4 iron, 4 sulfur cluster binding / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Phosphoribosyl transferase domain / NUDIX hydrolase / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain ...Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Phosphoribosyl transferase domain / NUDIX hydrolase / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
: / IRON/SULFUR CLUSTER / Amidophosphoribosyltransferase / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWitus, S.R.W. / Yang, Z. / Rape, M.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
American Cancer SocietyPF-24-1257623-01-TBE United States
CitationJournal: To Be Published
Title: Regulation of purine synthesis and chemotherapy response by metabolite-derived molecular glues
Authors: Witus, S.R.W. / Kober, M.M. / Roh, H. / Yang, Z. / Choueiry, F. / Ghate, A. / Titov, D.V. / Rape, M.
History
DepositionAug 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amidophosphoribosyltransferase
B: Amidophosphoribosyltransferase
C: Amidophosphoribosyltransferase
D: Amidophosphoribosyltransferase
E: ADP-sugar pyrophosphatase
F: ADP-sugar pyrophosphatase
G: ADP-sugar pyrophosphatase
H: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,08016
Polymers340,8568
Non-polymers3,2248
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Amidophosphoribosyltransferase / ATase / Glutamine phosphoribosylpyrophosphate amidotransferase / GPAT


Mass: 60690.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPAT, GPAT
Details (production host): pLVX-PPAT-V5-TwinStrep-IRES-puromycin
Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q06203, amidophosphoribosyltransferase
#2: Protein
ADP-sugar pyrophosphatase / 8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked ...8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked moiety X motif 5 / Nudix motif 5 / hNUDT5 / YSA1H


Mass: 24523.686 Da / Num. of mol.: 4 / Mutation: Y74F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5, NUDIX5, HSPC115 / Plasmid: pet28a / Details (production host): His-SUMO-TEV-NUDT5-Y74F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LOBSTR- -RIL
References: UniProt: Q9UKK9, ADP-ribose diphosphatase, 8-oxo-dGDP phosphatase, ADP-D-ribose pyrophosphorylase
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-A1CQ4 / 6-(benzylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine


Mass: 454.394 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H19N4O7PS / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
1Ternary complex of PPAT and NUDT5 with 6-benzylthioinosine-5'-monophosphateCOMPLEX#1-#20MULTIPLE SOURCES
2PPAT tetramerCOMPLEX#11RECOMBINANT1x PPAT tetramer per assembly
3NUDT5 dimerCOMPLEX#21RECOMBINANT2x NUDT5 dimers per assembly
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.33 MDaNO
210.232 MDaNO
310.049 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
11Homo sapiens (human)9606
22Homo sapiens (human)9606Expi293FpLVX-PPAT-V5-TwinStrep-IRES-puromycin
33Escherichia coli (E. coli)562LOBSTR-BL21(DE3)-RILpet28a-His-SUMO-TEV-NUDT5-Y74F
Buffer solutionpH: 7.5
Details: 25 mM HEPES pH 7.5, 150 mM NaCl, 2 mM 6-benzylthioinosine-5'-monophosphate, 1 mM DTT
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

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: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
2SerialEMimage acquisition
4cryoSPARC4.3CTF correction
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11ISOLDEmodel refinement
12cryoSPARC4.3initial Euler assignment
13cryoSPARC4.3final Euler assignment
14cryoSPARC4.3classification
15cryoSPARC4.33D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 502672 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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