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- EMDB-52600: Csu pilus rod antiparallel pair -

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Basic information

Entry
Database: EMDB / ID: EMD-52600
TitleCsu pilus rod antiparallel pair
Map dataCsu pilus rod pair map, sharpened, pixel spacing adjusted, cropped around the model
Sample
  • Complex: Csu pilus rod antiparallel pair
    • Protein or peptide: CsuA/B
Keywordspili / fimbriae / Acinetobacter baumannii pili / chaperone-usher pathway / archaic chaperone-usher pili / biofilm / 3D biofilm / adhesion / pathogenesis / pilus antiparallel binding junction / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.91 Å
AuthorsMalmi H / Pakharukova N / Zavialov AV
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 23, 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_52600.png

Downloads & links

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Map

FileDownload / File: emd_52600.map.gz / Format: CCP4 / Size: 2.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCsu pilus rod pair map, sharpened, pixel spacing adjusted, cropped around the model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.66 Å/pix.
x 44 pix.
= 73.154 Å		1.66 Å/pix.
x 71 pix.
= 118.045 Å		1.66 Å/pix.
x 211 pix.
= 350.809 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: 1.6626 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.37
Minimum - Maximum-0.11260743 - 2.039005
Average (Standard dev.)0.20234667 (±0.26300412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin11748129
Dimensions7121144
Spacing4471211
CellA: 73.1544 Å / B: 118.0446 Å / C: 350.8086 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52600_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Csu pilus rod pair map, sharpened, pixel spacing...

Fileemd_52600_additional_1.map
AnnotationCsu pilus rod pair 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 rod pair map, half map B, pixel spacing adjusted

Fileemd_52600_half_map_1.map
AnnotationCsu pilus rod pair map, half map B, pixel spacing adjusted
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Csu pilus rod pair map, half map A, pixel spacing adjusted

Fileemd_52600_half_map_2.map
AnnotationCsu pilus rod pair map, half map A, 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 antiparallel pair

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

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Supramolecule #1: Csu pilus rod antiparallel pair

SupramoleculeName: Csu pilus rod antiparallel pair / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Csu pilus rods are homopolymers of subunit CsuA/B. The sample contains Csu pilus rods self-assembled into pairs through antiparallel interactions.
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 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: 19096
Molecular weightTheoretical: 16.069642 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
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
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
170.0 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: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsCsu pilus rods are homopolymers of subunit CsuA/B. The sample contains Csu pilus rods self-assembled into pairs through antiparallel interactions. The pairs and stacks accumulate over time in a sample tube containing purified Csu pili.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / 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: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 35938
CTF correctionSoftware - Name: RELION (ver. 3.0)
Software - details: CTFFind-4.1 Micrographs with CTF fit better than 3.5 A were used for filament picking.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Software - details: Homogeneous Refinement / Number images used: 12883
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3) / Software - details: Ab Initio Reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.5.3) / Software - details: 2D Classification
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 first fit the subunits into the single native pilus rod map (PDB Accession ID: 9I37) and average their relative angles, and it was also used to adjust pixel spacing of all maps to match model dimensions. Coot was used to adjust side chain and loop positions. A pair of antiparallel pili with subunit angles adjusted to 3-turns-per-7-subunits symmetry was overlapped with a 2D class to adjust the binding junction angle. Finally, Phenix was used to fit the pair model into the map.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 304.76
Output model

PDB-9i3m:
Csu pilus rod antiparallel pair

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