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- EMDB-26546: Cryo-EM of self-assembled cannula CanA -

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Basic information

Entry
Database: EMDB / ID: EMD-26546
TitleCryo-EM of self-assembled cannula CanA
Map dataCryo-EM of self-assembled cannula CanA
Sample
  • Complex: CanA
    • Protein or peptide: CanA
  • Ligand: CALCIUM ION
  • Ligand: water
Keywordsself-assemble / cannula / helical tube / donor strand / PROTEIN FIBRIL
Biological speciesPyrodictium abyssi (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang F / Miller JG / Egelman EH / Conticello VP
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DMR-1533958 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: To Be Published
Title: Cryo-EM of self-assembled cannula CanA
Authors: Wang F / Miller JG / Egelman EH / Conticello VP
History
DepositionMar 29, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26546.png

Downloads & links

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Map

FileDownload / File: emd_26546.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of self-assembled cannula CanA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.7709993 - 1.440544
Average (Standard dev.)0.0069667813 (±0.07911987)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-224-224
Dimensions448448448
Spacing448448448
CellA=B=C: 483.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map A

Fileemd_26546_half_map_1.map
Annotationhalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map B

Fileemd_26546_half_map_2.map
Annotationhalf-map 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 : CanA

EntireName: CanA
Components
  • Complex: CanA
    • Protein or peptide: CanA
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: CanA

SupramoleculeName: CanA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrodictium abyssi (archaea)

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Macromolecule #1: CanA

MacromoleculeName: CanA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrodictium abyssi (archaea)
Molecular weightTheoretical: 19.989492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTQSPLNSF YATGTAQAVS EPIDVESHLG SITPAAGAQG SDDIGYAIVW IKDQVNDVKL KVTLANAEQL KPYFKYLQIQ ITSGYETNS TALGNFSETK AVISLDNPSA VIVLDKEDIA VLYPDKTGYT NTSIWVPGEP DKIIVYNETK PVAILNFKAF Y EAKEGMLF DSLPVIFNFQ VLQVG

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 2.5 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: 1.59 Å
Applied symmetry - Helical parameters - Δ&Phi: -173.747 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 659059
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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