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- EMDB-52601: Csu pilus rod type 1 stack -

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Basic information

Entry
Database: EMDB / ID: EMD-52601
TitleCsu pilus rod type 1 stack
Map dataCsu pilus type 1 antiparallel stack map, sharpened, pixel spacing adjusted, cropped around the model
Sample
  • Complex: Csu pilus rod type 1 stack
    • 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: 7.58 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_52601.png

Downloads & links

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Map

FileDownload / File: emd_52601.map.gz / Format: CCP4 / Size: 54.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCsu pilus type 1 antiparallel stack map, sharpened, pixel spacing adjusted, cropped around the model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 111 pix.
= 91.367 Å		0.82 Å/pix.
x 208 pix.
= 171.211 Å		0.82 Å/pix.
x 621 pix.
= 511.164 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: 0.82313 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.13744208 - 0.31232294
Average (Standard dev.)0.002925161 (±0.06888288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin25748305
Dimensions208621111
Spacing111208621
CellA: 91.36743 Å / B: 171.21104 Å / C: 511.16373 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52601_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Csu pilus type 1 antiparallel stack map, not...

Fileemd_52601_additional_1.map
AnnotationCsu pilus type 1 antiparallel stack map, not 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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Additional map: Csu pilus type 1 antiparallel stack map, sharpened,...

Fileemd_52601_additional_2.map
AnnotationCsu pilus type 1 antiparallel stack 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 type 1 antiparallel stack map, half...

Fileemd_52601_half_map_1.map
AnnotationCsu pilus type 1 antiparallel stack 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 type 1 antiparallel stack map, half...

Fileemd_52601_half_map_2.map
AnnotationCsu pilus type 1 antiparallel stack 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 type 1 stack

EntireName: Csu pilus rod type 1 stack
Components
  • Complex: Csu pilus rod type 1 stack
    • Protein or peptide: CsuA/B

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Supramolecule #1: Csu pilus rod type 1 stack

SupramoleculeName: Csu pilus rod type 1 stack / 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 type 1 and type 2 stack architectures through antiparallel interactions. The stacks ...Details: Csu pilus rods are homopolymers of subunit CsuA/B. The sample contains Csu pilus rods self-assembled into type 1 and type 2 stack architectures through antiparallel interactions. The stacks accumulate slowly over time as a gel-like substance at the bottom of a sample tube containing purified Csu pili.
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: Csu pilus rods are homopolymers of subunit CsuA/B. Structure depicts three Csu pilus rods forming type 1 stack architecture through antiparallel interactions.
Number of copies: 57 / 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 state2D array

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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 / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.014 kPa
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 type 1 and type 2 stack architectures through antiparallel interactions. The stacks accumulate slowly over time as a gel-like substance at the bottom of a sample tube containing purified Csu pili.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 7941 / Average exposure time: 2.79 sec. / Average electron dose: 59.848 e/Å2
Details: Grid squares and holes were selected manually as the pilus stacks were visible in the atlas.
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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 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: 30605819
Details: Two different types of Csu pilus stack architectures were solved from the same particle set. Particle picking failed to distinguish between the two, so the initial number of particles is the ...Details: Two different types of Csu pilus stack architectures were solved from the same particle set. Particle picking failed to distinguish between the two, so the initial number of particles is the same for both stack architectures.
CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.3) / Software - details: Patch CTF Correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: We used an earlier, unpublished 8.5 A map of Csu pilus type 1 stack as the starting model. It had been generated using Ab Initio reconstruction and another dataset.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Software - details: Local Refinement
Details: Local Refinement allowed generating a single map without individual particles flipping and settling into pseudosymmetric orientations.
Number images used: 504940
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Software - details: Homogeneous Refinement and Heterogeneous Refinement
Details: Homogeneous Refinement indicated that there are two types of stacks in the dataset. Generated masks based on an initial model overlapped with a 2D class allowed splitting the dataset between ...Details: Homogeneous Refinement indicated that there are two types of stacks in the dataset. Generated masks based on an initial model overlapped with a 2D class allowed splitting the dataset between the two stack architectures.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC (ver. v4.5.3) / Software - details: Heterogeneous Refinement
Details: The particles were too big for 3D Classification job, and the particles with Csu pilus stacks had a tendency to flip 180 degrees during refinement due to pseudosymmetries. We used models ...Details: The particles were too big for 3D Classification job, and the particles with Csu pilus stacks had a tendency to flip 180 degrees during refinement due to pseudosymmetries. We used models flipped 180 degrees in every direction as classes to collect the flipped particles and reorient them for local refinement. With the original model, six flipped models and one waste class, we had eight classes.
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 type 1 stack model into the map.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 668.1
Output model

PDB-9i3n:
Csu pilus rod type 1 stack

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