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- PDB-8yi9: human PRPS2 isoform2 -

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Basic information

Entry
Database: PDB / ID: 8yi9
Titlehuman PRPS2 isoform2
ComponentsIsoform 2 of Ribose-phosphate pyrophosphokinase 2
KeywordsLIGASE / Phosphoribosyl pyrophosphate synthetase
Function / homology
Function and homology information


5-Phosphoribose 1-diphosphate biosynthesis / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / 5-phosphoribose 1-diphosphate biosynthetic process / pentose-phosphate shunt / purine nucleotide biosynthetic process / nucleobase-containing compound metabolic process / kinase activity / magnesium ion binding ...5-Phosphoribose 1-diphosphate biosynthesis / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / 5-phosphoribose 1-diphosphate biosynthetic process / pentose-phosphate shunt / purine nucleotide biosynthetic process / nucleobase-containing compound metabolic process / kinase activity / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / Phosphoribosyl synthetase-associated domain / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 5-O-phosphono-beta-D-ribofuranose / Ribose-phosphate pyrophosphokinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu, J.L. / Lu, G.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 31771490 China
CitationJournal: To Be Published
Title: Structure of human PRPS2 long isoform at 3.4 Angstroms resolution.
Authors: Liu, J.L. / Lu, G.M.
History
DepositionFeb 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
B: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
C: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
D: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
E: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
F: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,82030
Polymers210,5846
Non-polymers4,23624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Isoform 2 of Ribose-phosphate pyrophosphokinase 2 / PPRibP / Phosphoribosyl pyrophosphate synthase II / PRS-II


Mass: 35097.398 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPS2 / Production host: Escherichia coli (E. coli)
References: UniProt: P11908, ribose-phosphate diphosphokinase
#2: Sugar
ChemComp-RP5 / 5-O-phosphono-beta-D-ribofuranose / [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE / 5-O-phosphono-beta-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
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

ComponentName: human Phosphoribosyl pyrophosphate synthetase hexamer with Ligands ADP,magnesium,and R5P.
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167321 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314142
ELECTRON MICROSCOPYf_angle_d0.64219176
ELECTRON MICROSCOPYf_dihedral_angle_d9.0912010
ELECTRON MICROSCOPYf_chiral_restr0.0462298
ELECTRON MICROSCOPYf_plane_restr0.0042418

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