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- EMDB-52812: Cryo-EM Structure of Self-assembled Zymomonas mobilis Levansucras... -

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Basic information

Entry
Database: EMDB / ID: EMD-52812
TitleCryo-EM Structure of Self-assembled Zymomonas mobilis Levansucrase Nanotube
Map data
Sample
  • Complex: Filamentus assembly of Z. mobilis Levansucrase
    • Protein or peptide: Levansucrase
  • Ligand: water
KeywordsZymomonas mobilis levansucrase / self-assembly / nanotube / TRANSFERASE
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)
Methodhelical reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsYu Y / Sonani RR / Hadad N / Salama R / Shoham G / Egelman E / Shoham Y / Danino D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM Structure of Self-assembled Zymomonas mobilis Levansucrase Nanotube
Authors: Yu Y / Sonani RR / Hadad N / Salama R / Shoham G / Egelman E / Shoham Y / Danino D
History
DepositionFeb 13, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52812.png

Downloads & links

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Map

FileDownload / File: emd_52812.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 437.76 Å		0.86 Å/pix.
x 512 pix.
= 437.76 Å		0.86 Å/pix.
x 512 pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.50230974 - 0.862686
Average (Standard dev.)-0.0003510451 (±0.026089141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52812_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52812_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 : Filamentus assembly of Z. mobilis Levansucrase

EntireName: Filamentus assembly of Z. mobilis Levansucrase
Components
  • Complex: Filamentus assembly of Z. mobilis Levansucrase
    • Protein or peptide: Levansucrase
  • Ligand: water

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Supramolecule #1: Filamentus assembly of Z. mobilis Levansucrase

SupramoleculeName: Filamentus assembly of Z. mobilis Levansucrase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Zymomonas mobilis subsp. mobilis ATCC 10988 (bacteria)

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Macromolecule #1: Levansucrase

MacromoleculeName: Levansucrase / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO / EC number: levansucrase
Source (natural)Organism: Zymomonas mobilis subsp. mobilis ATCC 10988 (bacteria)
Molecular weightTheoretical: 46.798703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLNKAGIAEP SLWTRADAMK VHTDDPTATM PTIDYDFPVM TDKYWVWDTW PLRDINGQVV SFQGWSVIFA LVADRTKYGW HNRNDGARI GYFYSRGGSN WIFGGHLLKD GANPRSWEWS GCTIMAPGTA NSVEVFFTSV NDTPSESVPA QCKGYIYADD K SVWFDGFD ...String:
MLNKAGIAEP SLWTRADAMK VHTDDPTATM PTIDYDFPVM TDKYWVWDTW PLRDINGQVV SFQGWSVIFA LVADRTKYGW HNRNDGARI GYFYSRGGSN WIFGGHLLKD GANPRSWEWS GCTIMAPGTA NSVEVFFTSV NDTPSESVPA QCKGYIYADD K SVWFDGFD KVTDLFQADG LYYADYAENN FWDFRDPHVF INPEDGKTYA LFEGNVAMER GTVAVGEEEI GPVPPKTETP DG ARYCAAA IGIAQALNEA RTEWKLLPPL VTAFGVNDQT ERPHVVFQNG LTYLFTISHH STYADGLSGP DGVYGFVSEN GIF GPYEPL NGSGLVLGNP SSQPYQAYSH YVMTNGLVTS FIDTIPSSDP NVYRYGGTLA PTIKLELVGH RSFVTEVKGY GYIP PQIEW LAEDESSNSA AALSLLNK

UniProtKB: Levansucrase

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1196 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 5.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 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: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 23.144 Å
Applied symmetry - Helical parameters - Δ&Phi: -163.328 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2457366
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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