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- EMDB-27291: Human PRPS1-E307A engineered mutation with Phosphate, ATP, and R5... -

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Basic information

Entry
Database: EMDB / ID: EMD-27291
TitleHuman PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P; Hexamer
Map dataHuman PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P, Hexamer Centered
Sample
  • Complex: Hexamer of phosphoribosyl pyrophosphate synthetase 1 E307A engineered mutation with phosphate, ATP, and R5P
    • Protein or peptide: Ribose-phosphate pyrophosphokinase 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-O-phosphono-alpha-D-ribofuranose
  • Ligand: MAGNESIUM ION
Keywordsphosphoribosyl pyrophosphate synthetase / ATP/R5P substrate / Filament-breaking mutation / TRANSFERASE
Function / homology
Function and homology information


5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process ...5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process / purine nucleobase metabolic process / kinase activity / nervous system development / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsHvorecny KL / Kollman JM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI145111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118396 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Human PRPS1 filaments stabilize allosteric sites to regulate activity.
Authors: Hvorecny KL / Hargett K / Quispe JD / Kollman JM
History
DepositionJun 14, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27291.png

Downloads & links

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Map

FileDownload / File: emd_27291.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P, Hexamer Centered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.64 Å		0.83 Å/pix.
x 320 pix.
= 264.64 Å		0.83 Å/pix.
x 320 pix.
= 264.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-10.984992999999999 - 17.929510000000001
Average (Standard dev.)0.000000000002593 (±0.34671462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human PRPS1-E307A engineered mutation with Phosphate, ATP, and...

Fileemd_27291_half_map_1.map
AnnotationHuman PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P, Hexamer Centered half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human PRPS1-E307A engineered mutation with Phosphate, ATP, and...

Fileemd_27291_half_map_2.map
AnnotationHuman PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P, Hexamer Centered half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexamer of phosphoribosyl pyrophosphate synthetase 1 E307A engine...

EntireName: Hexamer of phosphoribosyl pyrophosphate synthetase 1 E307A engineered mutation with phosphate, ATP, and R5P
Components
  • Complex: Hexamer of phosphoribosyl pyrophosphate synthetase 1 E307A engineered mutation with phosphate, ATP, and R5P
    • Protein or peptide: Ribose-phosphate pyrophosphokinase 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-O-phosphono-alpha-D-ribofuranose
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Hexamer of phosphoribosyl pyrophosphate synthetase 1 E307A engine...

SupramoleculeName: Hexamer of phosphoribosyl pyrophosphate synthetase 1 E307A engineered mutation with phosphate, ATP, and R5P
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Six copies of PRPS1-E307A assemble to form a hexamer.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ribose-phosphate pyrophosphokinase 1

MacromoleculeName: Ribose-phosphate pyrophosphokinase 1 / 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: 34.777086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SPNIKIFSGS SHQDLSQKIA DRLGLELGKV VTKKFSNQET CVEIGESVRG EDVYIVQSGC GEINDNLMEL LIMINACKIA SASRVTAVI PCFPYARQDK KDKSRAPISA KLVANMLSVA GADHIITMDL HASQIQGFFD IPVDNLYAEP AVLKWIRENI S EWRNCTIV ...String:
SPNIKIFSGS SHQDLSQKIA DRLGLELGKV VTKKFSNQET CVEIGESVRG EDVYIVQSGC GEINDNLMEL LIMINACKIA SASRVTAVI PCFPYARQDK KDKSRAPISA KLVANMLSVA GADHIITMDL HASQIQGFFD IPVDNLYAEP AVLKWIRENI S EWRNCTIV SPDAGGAKRV TSIADRLNVD FALIHKERKK ANEVDRMVLV GDVKDRVAIL VDDMADTCGT ICHAADKLLS AG ATRVYAI LTHGIFSGPA ISRINNACFE AVVVTNTIPQ EDKMKHCSKI QVIDISMILA EAIRRTHNGA SVSYLFSHVP L

UniProtKB: Ribose-phosphate pyrophosphokinase 1

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: 5-O-phosphono-alpha-D-ribofuranose

MacromoleculeName: 5-O-phosphono-alpha-D-ribofuranose / type: ligand / ID: 3 / Number of copies: 6 / Formula: HSX
Molecular weightTheoretical: 230.11 Da
Chemical component information

ChemComp-HSX:
5-O-phosphono-alpha-D-ribofuranose

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.6
GridModel: C-flat / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PHENIX (ver. 1.18) / Number images used: 810903
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8dbn:
Human PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P; Hexamer

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