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- EMDB-52587: Csu pilus rod purified from Acinetobacter baumannii -

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Basic information

Entry
Database: EMDB / ID: EMD-52587
TitleCsu pilus rod purified from Acinetobacter baumannii
Map dataCsu pilus native rod helical structure map, sharpened, pixel spacing adjusted, cropped around the model
Sample
  • Complex: Csu pilus rod
    • Protein or peptide: CsuA/B
Keywordspili / fimbriae / Acinetobacter baumannii pili / chaperone-usher pathway / archaic chaperone-usher pili / biofilm / 3D biofilm / adhesion / pathogenesis / CELL ADHESION
Function / homology: / Spore coat protein U / Spore Coat Protein U domain / Spore Coat Protein U domain / Spore coat protein U/FanG domain-containing protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsMalmi H / Zavialov AV / Pakharukova N
Funding support Finland, 3 items
OrganizationGrant numberCountry
Academy of Finland321762 Finland
Academy of Finland360760 Finland
Sigrid Juselius Foundation2023 Finland
CitationJournal: To Be Published
Title: Antiparallel stacking of Csu pili drives Acinetobacter baumannii 3D biofilm assembly
Authors: Malmi H / Pakharukova N / Paul B / Tuittila M / Ahmad I / Knight SD / Uhlin BE / Ghosal D / Zavialov AV
History
DepositionJan 22, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52587.png

Downloads & links

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Map

FileDownload / File: emd_52587.map.gz / Format: CCP4 / Size: 3.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCsu pilus native rod helical structure map, sharpened, pixel spacing adjusted, cropped around the model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 61 pix.
= 64.331 Å		1.05 Å/pix.
x 62 pix.
= 65.385 Å		1.05 Å/pix.
x 223 pix.
= 235.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.0546 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.23220225 - 0.44279343
Average (Standard dev.)0.008393941 (±0.04146377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin11922121
Dimensions6222361
Spacing6162223
CellA: 64.3306 Å / B: 65.3852 Å / C: 235.1758 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52587_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Csu pilus native rod helical structure map, sharpened,...

Fileemd_52587_additional_1.map
AnnotationCsu pilus native rod helical structure map, sharpened, pixel spacing adjusted, not cropped around the model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Csu pilus native rod helical structure map, half...

Fileemd_52587_half_map_1.map
AnnotationCsu pilus native rod helical structure map, half map A, pixel spacing adjusted
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Csu pilus native rod helical structure map, half...

Fileemd_52587_half_map_2.map
AnnotationCsu pilus native rod helical structure map, half map B, pixel spacing adjusted
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Csu pilus rod

EntireName: Csu pilus rod
Components
  • Complex: Csu pilus rod
    • Protein or peptide: CsuA/B

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Supramolecule #1: Csu pilus rod

SupramoleculeName: Csu pilus rod / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Csu pili extracted from Acinetobacter baumannii.
Source (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: 19096 / Tissue: Planktonic bacteria / Organelle: Outer membrane / Location in cell: Outer membrane
Molecular weightTheoretical: 16.05974 kDa/nm

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Macromolecule #1: CsuA/B

MacromoleculeName: CsuA/B / type: protein_or_peptide / ID: 1 / Details: Polymer of subunit CsuA/B. / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: 19096 / Tissue: bacterial surface
Molecular weightTheoretical: 16.069642 KDa
SequenceString:
AVTGQVDVKL NISTGCTVGG SQTEGNMNKF GTLNFGKTSG TWNNVLTAEV ASAATGGNIS VTCDGTDPVD FTVAIDGGER TDRTLKNTA SADVVAYNVY RDAARTNLYV VNQPQQFTTV SGQATAVPIF GAIAPNTGTP KAQGDYKDTL LVTVNF

UniProtKB: Spore coat protein U/FanG domain-containing 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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
125.0 mMNaClsodium chloride

Details: Sample is a fraction taken from an ion exchange column elution gradient, so the NaCl concentration may vary.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsExtracted from the bacterial outer membrane.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 54.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.606 Å
Applied symmetry - Helical parameters - Δ&Phi: -153.984 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 50502
CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.3)
Software - details: Patch CTF Micrographs with CTF fit better than 3.5 A were used for filament picking.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 189846 / Software - Name: cryoSPARC (ver. v4.5.3) / Software - details: Filament Tracer
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7zl4


Chain - Residue range: 24-178 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The initial model consisted of a single pilus rod fragment of the same type. The initial model in turn is based on a crystal structure of CsuA/Bsc with PDB accession code 6FM5.
DetailsUCSF Chimera was used to fit the subunits into the map and adjust their relative angles, and it was also used to adjust map pixel spacing to match model dimensions. Coot was used to adjust side chain and loop positions. Phenix was used to fit the final version of the model into the stack map.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 72.51
Output model

PDB-9i37:
Csu pilus rod purified from Acinetobacter baumannii

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