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- EMDB-46690: Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding D... -

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Basic information

Entry
Database: EMDB / ID: EMD-46690
TitleCryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
Map data
Sample
  • Complex: 24-meric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
    • Protein or peptide: Phosphoenolpyruvate synthase
  • Ligand: MAGNESIUM ION
Keywordsphosphoenolpyruvate / enzyme / multimeric / pyruvate / CYTOSOLIC PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsLegare S / Kirby MW / Stetefeld J
Funding support1 items
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 MW / Stetefeld J
History
DepositionAug 22, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46690.png

Downloads & links

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Map

FileDownload / File: emd_46690.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 392 pix.
= 403.76 Å		1.03 Å/pix.
x 392 pix.
= 403.76 Å		1.03 Å/pix.
x 392 pix.
= 403.76 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.04
Minimum - Maximum-0.040112827 - 0.17825322
Average (Standard dev.)-0.00019413757 (±0.0064176884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 403.75998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46690_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46690_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46690_half_map_2.map
Projections & Slices
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Sample components

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Entire : 24-meric Phosphoenolpyruvate Binding Domain of Staphylothermus ma...

EntireName: 24-meric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
Components
  • Complex: 24-meric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
    • Protein or peptide: Phosphoenolpyruvate synthase
  • Ligand: MAGNESIUM ION

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Supramolecule #1: 24-meric Phosphoenolpyruvate Binding Domain of Staphylothermus ma...

SupramoleculeName: 24-meric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Staphylothermus marinus F1 (archaea)
Molecular weightTheoretical: 888.24 kDa/nm

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Macromolecule #1: Phosphoenolpyruvate synthase

MacromoleculeName: Phosphoenolpyruvate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: pyruvate, water dikinase
Source (natural)Organism: Staphylothermus marinus F1 (archaea) / Strain: F1
Molecular weightTheoretical: 95.153914 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGSNVPKEK RFIVWLDEVT KDDVVLVGGK NANLGEMIRA GIPVPPGFAV TAYAYKYFIE KTGLKDKIYP LLNSIDVND KKVLDETTAK IRQWIMDTPM PPEVEEEIRK YYRELAKKIG MEPEKLRVAV RSSATAEDMP EASFAGQQDT Y LNVYGEDN ...String:
MGSSHHHHHH SSGSNVPKEK RFIVWLDEVT KDDVVLVGGK NANLGEMIRA GIPVPPGFAV TAYAYKYFIE KTGLKDKIYP LLNSIDVND KKVLDETTAK IRQWIMDTPM PPEVEEEIRK YYRELAKKIG MEPEKLRVAV RSSATAEDMP EASFAGQQDT Y LNVYGEDN VVYYVKRCWA SLFTSRAVFY RVAQGIPHEK SLMSVTVQKM VNSRTAGVMF TLHPVTGDEK VVVIEASWGL GE SVVGGKV TPDEWVVDKQ TLQIVDQKIH HKTLAIVFDP KKGKNVEIRW DENKQAWVSE EGPVDIEMVK HFHPDKPALK EEE VKRLAE LALLIEKHYG RHMDIEWAVD YDIPFPDNVF IVQARLETVW SVRKEKEKAE KKAEIKGKNI VKLSEAKVLV RGLP ASPGI GAGVAKVIFD PHSKEAQEFK EGEVLVTKMT DPDWVPLMKK AVAIVTDEGG MTSHAAIVSR ELGIPAIVGT GNATQ VIKS GIEVTVDGSR GVVYEGIVED LVKPKEEVKA EVAGVGISPE QLLPLYPVTA TKIYMNLGEP DAIEKYKDLP FDGIGL MRI EFIITDWVQY HPLYLIEQGK ESLFIDKLAE GIAKVAQAIY PRPVVVRFSD FKTNEYRGLK GGEKYEPEER NPMIGWR GV SRYIHPKYEP AFRLEVRAIK KVREEMGLTN VWVMFPFVRT TWELERALKI MEEEGLKRGK DFKVWAMAEV PSIVLLAD K FAEYVDGFSI GSNDLTQLIL GADRDSNILA EMGYFDERDP AVLAGIKMII EKAHSKGATV SICGQAPSVY PEIVEFLVE AGIDSISVNP DAVIATRRLV ASIERKIMLK RLNKIMDKLN KLELGF

UniProtKB: Probable phosphoenolpyruvate synthase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 24 / 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 stateparticle

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Sample preparation

Concentration1.9 mg/mL
BufferpH: 7.3
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMNaCl
10.0 mMMgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.12 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio from cryoSPARC
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 1138254
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 4.5.3)
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: FLEXIBLE FIT
Output model

PDB-9dae:
Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase

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