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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | PPSA C terminal octahedral structure | |||||||||
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![]() | enzyme / phosphorylation of pyruvate / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | ![]() pyruvate, water dikinase / pyruvate, water dikinase activity / pyruvate metabolic process / gluconeogenesis / phosphorylation / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Song W | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Survival strategies in the heat Lysine acetylation stabilizes the quaternary structure of a Mega-Dalton hyperthermophilic PEP-synthase Authors: Song W | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.7 KB 14.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.5 KB | Display | ![]() |
Images | ![]() | 211.8 KB | ||
Masks | ![]() | 52.7 MB | ![]() | |
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 36.8 MB 36.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 687.4 KB | Display | ![]() |
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Full document | ![]() | 686.9 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a8eMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Phosphoenolpyruvate synthase
Entire | Name: Phosphoenolpyruvate synthase |
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Components |
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-Supramolecule #1: Phosphoenolpyruvate synthase
Supramolecule | Name: Phosphoenolpyruvate synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.3 MDa |
-Macromolecule #1: Phosphoenolpyruvate synthase
Macromolecule | Name: Phosphoenolpyruvate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: pyruvate, water dikinase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 90.600922 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Sugar embedding | Material: Ice Details: The sample was plunged freeze in ethane-propane and transfer to liquid nitrogen. | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | ![]() PDB-8a8e: |