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- EMDB-39312: human PRPS2 isoform2 -

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Basic information

Entry
Database: EMDB / ID: EMD-39312
Titlehuman PRPS2 isoform2
Map data
Sample
  • Complex: human Phosphoribosyl pyrophosphate synthetase hexamer with Ligands ADP,magnesium,and R5P.
    • Protein or peptide: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
  • Ligand: 5-O-phosphono-beta-D-ribofuranose
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsPhosphoribosyl pyrophosphate synthetase / LIGASE
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 / cytosol / cytoplasm
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
Ribose-phosphate pyrophosphokinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu JL / Lu GM
Funding support China, 1 items
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 JL / Lu GM
History
DepositionFeb 29, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39312.png

Downloads & links

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Map

FileDownload / File: emd_39312.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 150 pix.
= 159. Å		1.06 Å/pix.
x 150 pix.
= 159. Å		1.06 Å/pix.
x 150 pix.
= 159. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034
Minimum - Maximum-0.15601316 - 0.23705192
Average (Standard dev.)-0.00013550303 (±0.014232346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 158.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39312_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_39312_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39312_half_map_2.map
Projections & Slices
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Sample components

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Entire : human Phosphoribosyl pyrophosphate synthetase hexamer with Ligand...

EntireName: human Phosphoribosyl pyrophosphate synthetase hexamer with Ligands ADP,magnesium,and R5P.
Components
  • Complex: human Phosphoribosyl pyrophosphate synthetase hexamer with Ligands ADP,magnesium,and R5P.
    • Protein or peptide: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
  • Ligand: 5-O-phosphono-beta-D-ribofuranose
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: human Phosphoribosyl pyrophosphate synthetase hexamer with Ligand...

SupramoleculeName: human Phosphoribosyl pyrophosphate synthetase hexamer with Ligands ADP,magnesium,and R5P.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Ribose-phosphate pyrophosphokinase 2

MacromoleculeName: Isoform 2 of Ribose-phosphate pyrophosphokinase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: ribose-phosphate diphosphokinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.097398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPNIVLFSGS SHQDLSQRVA DRLGLELGKV VTKKFSNQET SVEIGESVRG EDVYIIQSGC GEINDNLMEL LIMINACKIA SSSRVTAVI PCFPYARQDK KDKVGESRAP ISAKLVANML SVAGADHIIT MDLHASQIQG FFDIPVDNLY AEPAVLQWIR E NIAEWKNC ...String:
MPNIVLFSGS SHQDLSQRVA DRLGLELGKV VTKKFSNQET SVEIGESVRG EDVYIIQSGC GEINDNLMEL LIMINACKIA SSSRVTAVI PCFPYARQDK KDKVGESRAP ISAKLVANML SVAGADHIIT MDLHASQIQG FFDIPVDNLY AEPAVLQWIR E NIAEWKNC IIVSPDAGGA KRVTSIADRL NVEFALIHKE RKKANEVDRM VLVGDVKDRV AILVDDMADT CGTICHAADK LL SAGATKV YAILTHGIFS GPAISRINNA AFEAVVVTNT IPQEDKMKHC TKIQVIDISM ILAEAIRRTH NGESVSYLFS HVP L

UniProtKB: Ribose-phosphate pyrophosphokinase 2

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Macromolecule #2: 5-O-phosphono-beta-D-ribofuranose

MacromoleculeName: 5-O-phosphono-beta-D-ribofuranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: RP5
Molecular weightTheoretical: 230.11 Da
Chemical component information

ChemComp-RP5:
5-O-phosphono-beta-D-ribofuranose

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 167321
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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