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- EMDB-15230: PPSA C terminal octahedral structure -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-15230
TitlePPSA C terminal octahedral structure
Map data
Sample
  • Complex: Phosphoenolpyruvate synthase
    • Protein or peptide: Phosphoenolpyruvate synthase
Keywordsenzyme / phosphorylation of pyruvate / BIOSYNTHETIC 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
Phosphoenolpyruvate synthase
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSong W
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Survival strategies in the heat Lysine acetylation stabilizes the quaternary structure of a Mega-Dalton hyperthermophilic PEP-synthase
Authors: Song W
History
DepositionJun 22, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15230.png

Downloads & links

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Map

FileDownload / File: emd_15230.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0709
Minimum - Maximum-0.08230619 - 0.26874745
Average (Standard dev.)0.0033085863 (±0.014292836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15230_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15230_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15230_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phosphoenolpyruvate synthase

EntireName: Phosphoenolpyruvate synthase
Components
  • Complex: Phosphoenolpyruvate synthase
    • Protein or peptide: Phosphoenolpyruvate synthase

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Supramolecule #1: Phosphoenolpyruvate synthase

SupramoleculeName: Phosphoenolpyruvate synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 2.3 MDa

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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: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 90.600922 KDa
Recombinant expressionOrganism: Pyrococcus furiosus DSM 3638 (archaea)
SequenceString: MAYRFIKWFE ELSKNDVPLV GGKGANLGEM TNAGIPVPPG FCVTAEAYKY FVENVKVSKE DVKRILGEKV NKGTISEVLA QAPDEPRPL QDWIMDIISK TDVDDSKMLQ ENTEAIRTLI KSLDMPSEIA EEIKQAYKEL SQRFGQEEVY VAVRSSATAE D LPEASFAG ...String:
MAYRFIKWFE ELSKNDVPLV GGKGANLGEM TNAGIPVPPG FCVTAEAYKY FVENVKVSKE DVKRILGEKV NKGTISEVLA QAPDEPRPL QDWIMDIISK TDVDDSKMLQ ENTEAIRTLI KSLDMPSEIA EEIKQAYKEL SQRFGQEEVY VAVRSSATAE D LPEASFAG QQETYLDVLG ADDVIDKVKR CWASLWTARA TFYRAKQGFD HSKVYLSAVV QKMVNSEKSG VMFTANPVTN NR NEIMINA SWGLGEAVVS GAVTPDEYIV EKGTWKIKEK VIAKKEVMVI RNPETGRGTV MVKVAEYLGP EWVEKQVLTD EQI IEVAKM GQKIEDHYGW PQDIEWAYDK DDGKLYIVQS RPITTLKEEA TAEEAEEVEE AEVILKGLGA SPGIGAGRVV VIFD ASEID KVKEGDILVT TMTNPDMVPA MKRAAAIVTD EGGRTSHAAI VSRELGIPCV VGTKEATKKL KTGMYVTVDG TRGLV YKGI VKSLVKKKEE AKAEGGQVVV AGAPLVTGTM VKVNVSMPEV AERAAATGAD GVGLLRAEHM ILSIGQHPIK FIKEGK EEE LVEKLAEGIE KVAAAFYPRP VWYRTLDAPT NEFREMPGGE DEPEERNPML GWRGIRRGLD QPELLRAEFK AIKKVVE KG YNNIGVMLPL VSHPEQIREA KRIAREVGLE PHKDVAWGVM IEVPAAAIII EDLIKEGIDF VSFGTNDLTQ YTLAIDRD N ERVAKLYDET HPAVLKLIKH VIKVCKRYGV ETSICGQAGS DPKMARILVR LGIDSISANP DAVQLIRQVV AQEERKLML EAARKQLFEE EEEEELF

UniProtKB: Phosphoenolpyruvate synthase

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
2.0 mMMgCl2Magnesium chloride
25.0 mMHEPESHEPES sodium salt
Sugar embeddingMaterial: Ice
Details: The sample was plunged freeze in ethane-propane and transfer to liquid nitrogen.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298.15 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: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142247
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-8a8e:
PPSA C terminal octahedral structure

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