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- EMDB-44895: Cryo-EM structure of extracellular tube from Microcystis Aerugino... -

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Basic information

Entry
Database: EMDB / ID: EMD-44895
TitleCryo-EM structure of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Map datacryo-EM map of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Sample
  • Complex: pili filaments
    • Protein or peptide: pilin
Keywordsextracellular tube / filament / pili / helical symmetry / PROTEIN FIBRIL
Function / homologyUncharacterized protein
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806SL (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsPetersen HA / Ricca JG / Louda JW / Wang F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Authors: Petersen HA / Ricca JG / Louda JW / Wang F
History
DepositionMay 15, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44895.png

Downloads & links

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Map

FileDownload / File: emd_44895.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.27
Minimum - Maximum-0.5425083 - 18.764292000000001
Average (Standard dev.)0.112361394 (±0.8750982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap A

Fileemd_44895_half_map_1.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_44895_half_map_2.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pili filaments

EntireName: pili filaments
Components
  • Complex: pili filaments
    • Protein or peptide: pilin

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Supramolecule #1: pili filaments

SupramoleculeName: pili filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Microcystis aeruginosa PCC 7806SL (bacteria)

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Macromolecule #1: pilin

MacromoleculeName: pilin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Microcystis aeruginosa PCC 7806SL (bacteria)
Molecular weightTheoretical: 15.515277 KDa
SequenceString:
MKASNYQEIA KAAILAGGLA AAGVLSVGES AQAQFIGTAS QSRVSAAVTS ILTDGNAAAT NSFAVEQVLP SSDYVFSGVV AVQVSYATT ISVGVGTAGA LTPVITAAEL TAPVVVNAGT QLTVERATAD AISKAATGSR FGDVSGIVRA WSAGTSVLD

UniProtKB: Uncharacterized protein

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.69 Å
Applied symmetry - Helical parameters - Δ&Phi: -14.74 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1875465
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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