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

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Basic information

Entry
Database: PDB / ID: 9i37
TitleCsu pilus rod purified from Acinetobacter baumannii
ComponentsCsuA/B
KeywordsCELL ADHESION / pili / fimbriae / Acinetobacter baumannii pili / chaperone-usher pathway / archaic chaperone-usher pili / biofilm / 3D biofilm / adhesion / pathogenesis
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsMalmi, H. / Zavialov, A.V. / Pakharukova, N.
Funding support Finland, 3items
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, S.D. / Uhlin, B.E. / Ghosal, D. / Zavialov, A.V.
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CsuA/B
B: CsuA/B
C: CsuA/B
D: CsuA/B
E: CsuA/B
F: CsuA/B
G: CsuA/B
H: CsuA/B
I: CsuA/B


Theoretical massNumber of molelcules
Total (without water)144,6279
Polymers144,6279
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
CsuA/B


Mass: 16069.642 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Details: Polymer of subunit CsuA/B. / Source: (natural) Acinetobacter baumannii (bacteria) / Plasmid details: chromosome / Strain: 19096 / Tissue: bacterial surface / References: UniProt: A0A6F8TDQ5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Csu pilus rod / Type: COMPLEX / Details: Csu pili extracted from Acinetobacter baumannii. / Entity ID: all / Source: NATURAL
Molecular weightValue: 16.05974 kDa/nm / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: 19096 / Cellular location: Outer membrane / Organelle: Outer membrane / Tissue: Planktonic bacteria
Buffer solutionpH: 7.4
Details: Sample is a fraction taken from an ion exchange column elution gradient, so the NaCl concentration may vary.
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2125 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Extracted from the bacterial outer membrane.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv4.5.3particle selectionFilament Tracer
2LatitudeSimage acquisitionLatitude-S (Gatan)
4cryoSPARCv4.5.3CTF correctionPatch CTF Micrographs with CTF fit better than 3.5 A were used for filament picking.
7UCSF Chimera1.15model fittingUCSF 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.
8Coot0.8.9.2 ELmodel fittingCoot was used to adjust side chain and loop positions.
13cryoSPARCv4.5.33D reconstruction
14PHENIX1.20.1_4487:model refinementPhenix was used to fit the final version of the model into the stack map.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -153.984 ° / Axial rise/subunit: 27.606 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 189846
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50502 / Symmetry type: HELICAL
Atomic model buildingB value: 72.51 / Protocol: RIGID BODY FIT / Space: REAL
Details: UCSF 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 ...Details: UCSF 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.
Atomic model buildingPDB-ID: 7ZL4

7zl4


Accession code: 7ZL4 / Chain residue range: 24-178
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.
Pdb chain residue range: 24-178 / Source name: PDB / Type: experimental model

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