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- EMDB-75440: Cryo-EM of chaperon usher pathway pilus from Stenotrophomonas mal... -

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Basic information

Entry
Database: EMDB / ID: EMD-75440
TitleCryo-EM of chaperon usher pathway pilus from Stenotrophomonas maltophilia
Map dataCryo-EM of chaperon usher pathway pilus from Stenotrophomonas maltophilia
Sample
  • Complex: pilus
    • Protein or peptide: Ferrous iron transporter B
Keywordspili / chaperon usher pathway pili / filament / PROTEIN FIBRIL
Function / homology:
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsFields JL / Zhang H / Wu H / Wang F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM159704 United States
CitationJournal: To Be Published
Title: Cryo-EM of chaperon usher pathway pilus from Stenotrophomonas maltophilia
Authors: Fields JL / Zhang H / Wu H / Wang F
History
DepositionFeb 6, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75440.png

Downloads & links

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Map

FileDownload / File: emd_75440.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of chaperon usher pathway pilus from Stenotrophomonas maltophilia
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.78
Minimum - Maximum-0.15318528 - 14.325144999999999
Average (Standard dev.)0.03437436 (±0.43973416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_75440_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_75440_half_map_2.map
Annotationhalf 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 : pilus

EntireName: pilus
Components
  • Complex: pilus
    • Protein or peptide: Ferrous iron transporter B

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Supramolecule #1: pilus

SupramoleculeName: pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Stenotrophomonas maltophilia (bacteria)

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Macromolecule #1: Ferrous iron transporter B

MacromoleculeName: Ferrous iron transporter B / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Stenotrophomonas maltophilia (bacteria)
Molecular weightTheoretical: 18.339422 KDa
SequenceString:
MHKINLIAAL MLAAAPLAAN AADGTITFNG KVTDKTCTIS TPGGKDFAVN LPTVSKNTLA TAGAVAGRTP FAINLTKCSA GNVATYFEP GSTVDFNSGR LVNQASANAA NNVQLQLLGS NNQFLPIKAA GAGQAQTNSQ WVAVGTDGSA DLNYYAEYYA T AAATPGDV TSSVKYTIIY N

UniProtKB: UNIPROTKB: A0AAD0BPX2

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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
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: 131.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -41 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: The helical symmetry for a single filament is C1, 26.6 A rise, and -152.2 deg twist. This is not applied to the deposited volume. There is a global symmetry for two filaments, which was not ...Details: The helical symmetry for a single filament is C1, 26.6 A rise, and -152.2 deg twist. This is not applied to the deposited volume. There is a global symmetry for two filaments, which was not applied in the reconstruction. The symmetry is D1, with a twist around -41 deg and a rise around 131.8 A.
Number images used: 85928
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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