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- EMDB-72100: Cryo-EM structure of PPAT-NUDT5 complex bound to 6-methylthioinos... -

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Basic information

Entry
Database: EMDB / ID: EMD-72100
TitleCryo-EM structure of PPAT-NUDT5 complex bound to 6-methylthioinosine-5'-monophosphate (6-meTIMP)
Map dataPPAT-NUDT5-6meTIMP sharpened map
Sample
  • Complex: Ternary complex of PPAT and NUDT5 with 6-methylthioinosine-5'-monophosphate
    • Complex: PPAT tetramer
      • Protein or peptide: Amidophosphoribosyltransferase
    • Complex: NUDT5 dimer
      • Protein or peptide: ADP-sugar pyrophosphatase
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 6-(methylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
KeywordsPurine synthesis / phosphoribosyltransferase / BIOSYNTHETIC PROTEIN
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
Amidophosphoribosyltransferase / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWitus SRW / Yang Z / Rape M
Funding support United States, 2 items
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 SRW / Kober MM / Roh H / Yang Z / Choueiry F / Ghate A / Titov DV / Rape M
History
DepositionAug 13, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72100.png

Downloads & links

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Map

FileDownload / File: emd_72100.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPPAT-NUDT5-6meTIMP sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.088 Å		0.85 Å/pix.
x 256 pix.
= 217.088 Å		0.85 Å/pix.
x 256 pix.
= 217.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.3353649 - 2.0851893
Average (Standard dev.)0.000818137 (±0.08383552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72100_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: PPAT-NUDT5-6meTIMP unsharpened map

Fileemd_72100_additional_1.map
AnnotationPPAT-NUDT5-6meTIMP unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PPAT-NUDT5-6meTIMP half map B

Fileemd_72100_half_map_1.map
AnnotationPPAT-NUDT5-6meTIMP half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PPAT-NUDT5-6meTIMP half map A

Fileemd_72100_half_map_2.map
AnnotationPPAT-NUDT5-6meTIMP half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of PPAT and NUDT5 with 6-methylthioinosine-5'-mon...

EntireName: Ternary complex of PPAT and NUDT5 with 6-methylthioinosine-5'-monophosphate
Components
  • Complex: Ternary complex of PPAT and NUDT5 with 6-methylthioinosine-5'-monophosphate
    • Complex: PPAT tetramer
      • Protein or peptide: Amidophosphoribosyltransferase
    • Complex: NUDT5 dimer
      • Protein or peptide: ADP-sugar pyrophosphatase
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 6-(methylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine

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Supramolecule #1: Ternary complex of PPAT and NUDT5 with 6-methylthioinosine-5'-mon...

SupramoleculeName: Ternary complex of PPAT and NUDT5 with 6-methylthioinosine-5'-monophosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49 KDa

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Supramolecule #2: PPAT tetramer

SupramoleculeName: PPAT tetramer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: 1x PPAT tetramer per assembly
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: NUDT5 dimer

SupramoleculeName: NUDT5 dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: 2x NUDT5 dimers per assembly
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Amidophosphoribosyltransferase

MacromoleculeName: Amidophosphoribosyltransferase / type: protein_or_peptide / ID: 1
Details: PPAT-V5-TwinStrep construct with N-terminal pro-peptide absent
Number of copies: 4 / Enantiomer: LEVO / EC number: amidophosphoribosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.690281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CGVFGCIASG EWPTQLDVPH VITLGLVGLQ HRGQESAGIV TSDGSSVPTF KSHKGMGLVN HVFTEDNLKK LYVSNLGIGH TRYATTGKC ELENCQPFVV ETLHGKIAVA HNGELVNAAR LRKKLLRHGI GLSTSSDSEM ITQLLAYTPP QEQDDTPDWV A RIKNLMKE ...String:
CGVFGCIASG EWPTQLDVPH VITLGLVGLQ HRGQESAGIV TSDGSSVPTF KSHKGMGLVN HVFTEDNLKK LYVSNLGIGH TRYATTGKC ELENCQPFVV ETLHGKIAVA HNGELVNAAR LRKKLLRHGI GLSTSSDSEM ITQLLAYTPP QEQDDTPDWV A RIKNLMKE APTAYSLLIM HRDVIYAVRD PYGNRPLCIG RLIPVSDIND KEKKTSETEG WVVSSESCSF LSIGARYYRE VL PGEIVEI SRHNVQTLDI ISRSEGNPVA FCIFEYVYFA RPDSMFEDQM VYTVRYRCGQ QLAIEAPVDA DLVSTVPESA TPA ALAYAG KCGLPYVEVL CKNRYVGRTF IQPNMRLRQL GVAKKFGVLS DNFKGKRIVL VDDSIVRGNT ISPIIKLLKE SGAK EVHIR VASPPIKYPC FMGINIPTKE ELIANKPEFD HLAEYLGANS VVYLSVEGLV SSVQEGIKFK KQKEKKHDIM IQENG NGLE CFEKSGHCTA CLTGKYPVEL EWGGSKPIPN PLLGLDSTSA WSHPQFEKGG GSGGGSGGGA WSHPQFEK

UniProtKB: Amidophosphoribosyltransferase

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Macromolecule #2: ADP-sugar pyrophosphatase

MacromoleculeName: ADP-sugar pyrophosphatase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: ADP-ribose diphosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.523686 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GGGSGESQEP TESSQNGKQY IISEELISEG KWVKLEKTTY MDPTGKTRTW ESVKRTTRKE QTADGVAVIP VLQRTLHFEC IVLVKQFRP PMGGYCIEFP AGLIDDGETP EAAALRELEE ETGYKGDIAE CSPAVCMDPG LSNCTIHIVT VTINGDDAEN A RPKPKPGD ...String:
GGGSGESQEP TESSQNGKQY IISEELISEG KWVKLEKTTY MDPTGKTRTW ESVKRTTRKE QTADGVAVIP VLQRTLHFEC IVLVKQFRP PMGGYCIEFP AGLIDDGETP EAAALRELEE ETGYKGDIAE CSPAVCMDPG LSNCTIHIVT VTINGDDAEN A RPKPKPGD GEFVEVISLP KNDLLQRLDA LVAEEHLTVD ARVYSYALAL KHANAKPFEV PFLKF

UniProtKB: ADP-sugar pyrophosphatase

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Macromolecule #3: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 3 / Number of copies: 4 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #4: 6-(methylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine

MacromoleculeName: 6-(methylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
type: ligand / ID: 4 / Number of copies: 4 / Formula: A1CQ3
Molecular weightTheoretical: 378.298 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Details: 25 mM HEPES pH 7.5, 150 mM NaCl, 2mM 6-methylthioinosine-5'-monophosphate, 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.3) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 967122
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9q0n:
Cryo-EM structure of PPAT-NUDT5 complex bound to 6-methylthioinosine-5'-monophosphate (6-meTIMP)

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