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- PDB-9dae: Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding D... -

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Basic information

Entry
Database: PDB / ID: 9dae
TitleCryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
ComponentsPhosphoenolpyruvate synthase
KeywordsCYTOSOLIC PROTEIN / phosphoenolpyruvate / enzyme / multimeric / pyruvate
Function / homology
Function and homology information


pyruvate, water dikinase / pyruvate, water dikinase activity / gluconeogenesis / ATP binding / metal ion binding
Similarity search - Function
Phosphoenolpyruvate synthase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain ...Phosphoenolpyruvate synthase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / ATP-grasp fold, subdomain 1
Similarity search - Domain/homology
Probable phosphoenolpyruvate synthase
Similarity search - Component
Biological speciesStaphylothermus marinus F1 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsLegare, S. / Kirby, M.W. / Stetefeld, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
Authors: Legare, S. / Kirby, M.W. / Stetefeld, J.
History
DepositionAug 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data 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: Phosphoenolpyruvate synthase
C: Phosphoenolpyruvate synthase
E: Phosphoenolpyruvate synthase
G: Phosphoenolpyruvate synthase
I: Phosphoenolpyruvate synthase
K: Phosphoenolpyruvate synthase
M: Phosphoenolpyruvate synthase
O: Phosphoenolpyruvate synthase
Q: Phosphoenolpyruvate synthase
S: Phosphoenolpyruvate synthase
V: Phosphoenolpyruvate synthase
X: Phosphoenolpyruvate synthase
Z: Phosphoenolpyruvate synthase
BA: Phosphoenolpyruvate synthase
DA: Phosphoenolpyruvate synthase
FA: Phosphoenolpyruvate synthase
HA: Phosphoenolpyruvate synthase
JA: Phosphoenolpyruvate synthase
LA: Phosphoenolpyruvate synthase
NA: Phosphoenolpyruvate synthase
PA: Phosphoenolpyruvate synthase
RA: Phosphoenolpyruvate synthase
TA: Phosphoenolpyruvate synthase
VA: Phosphoenolpyruvate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,284,27748
Polymers2,283,69424
Non-polymers58324
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 ...
Phosphoenolpyruvate synthase / PEP synthase / Pyruvate / water dikinase


Mass: 95153.914 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylothermus marinus F1 (archaea) / Strain: F1 / Gene: ppsA, Smar_0141 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P46893, pyruvate, water dikinase
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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: 24-meric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 888.24 kDa/nm / Experimental value: NO
Source (natural)Organism: Staphylothermus marinus F1 (archaea)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.3
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2150 mMNaCl1
310 mMMgCl21
SpecimenConc.: 1.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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 magnification: 75000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 42 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2EPUimage acquisition
4cryoSPARC4.5.3CTF correction
9PHENIX1.21.1-5286_5286:model refinement
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1138254 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00263552
ELECTRON MICROSCOPYf_angle_d0.49885872
ELECTRON MICROSCOPYf_dihedral_angle_d3.6348496
ELECTRON MICROSCOPYf_chiral_restr0.0429480
ELECTRON MICROSCOPYf_plane_restr0.00510944

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