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- PDB-9ibs: Cryo-EM Structure of Self-assembled Zymomonas mobilis Levansucras... -

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Basic information

Entry
Database: PDB / ID: 9ibs
TitleCryo-EM Structure of Self-assembled Zymomonas mobilis Levansucrase Nanotube
ComponentsLevansucrase
KeywordsTRANSFERASE / Zymomonas mobilis levansucrase / self-assembly / nanotube
Function / homologylevansucrase / levansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / extracellular region / Levansucrase
Function and homology information
Biological speciesZymomonas mobilis subsp. mobilis ATCC 10988 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsYu, Y. / Sonani, R.R. / Hadad, N. / Salama, R. / Shoham, G. / Egelman, E. / Shoham, Y. / Danino, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM Structure of Self-assembled Zymomonas mobilis Levansucrase Nanotube
Authors: Yu, Y. / Sonani, R.R. / Hadad, N. / Salama, R. / Shoham, G. / Egelman, E. / Shoham, Y. / Danino, D.
History
DepositionFeb 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Levansucrase
B: Levansucrase
C: Levansucrase
E: Levansucrase
G: Levansucrase
H: Levansucrase
J: Levansucrase
K: Levansucrase
M: Levansucrase
N: Levansucrase
P: Levansucrase
Q: Levansucrase
S: Levansucrase
T: Levansucrase
V: Levansucrase
W: Levansucrase


Theoretical massNumber of molelcules
Total (without water)748,77916
Polymers748,77916
Non-polymers00
Water21,5461196
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
Levansucrase / Beta-D-fructofuranosyl transferase / Sucrose 6-fructosyl transferase


Mass: 46798.703 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ATCC 10988 (bacteria)
Gene: sacB, levU, Zmob_0914 / Production host: Escherichia coli (E. coli) / References: UniProt: F8DT26, levansucrase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1196 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filamentus assembly of Z. mobilis Levansucrase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Zymomonas mobilis subsp. mobilis ATCC 10988 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 5.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -163.328 ° / Axial rise/subunit: 23.144 Å / Axial symmetry: D1
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2457366 / Symmetry type: HELICAL

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