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- PDB-9hpz: Cryo-EM structure of the wild-type flagellar filament from Rosebu... -

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Basic information

Entry
Database: PDB / ID: 9hpz
TitleCryo-EM structure of the wild-type flagellar filament from Roseburia hominis
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / Flagellin / Helical / Filament / Commensal
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesRoseburia hominis A2-183 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsBell, M.E.W. / Koch, I. / Hipp, K. / Hartmann, M.D. / Merino, F. / Ley, R.E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of the wild-type flagellar filament from Roseburia hominis
Authors: Bell, M.E.W. / Ley, R.E.
History
DepositionDec 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 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: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
V: Flagellin


Theoretical massNumber of molelcules
Total (without water)629,65722
Polymers629,65722
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 ...
Flagellin


Mass: 28620.791 Da / Num. of mol.: 22 / Source method: isolated from a natural source
Details: Complex comprised of identical flagellin monomers. The density lacked the hyper-variable domains, which were omitted from structure building.
Source: (natural) Roseburia hominis A2-183 (bacteria) / References: UniProt: G2SZK6
Has protein modificationN

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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: Wild-type flagellar filament of the commensal bacteria Roseburia hominis
Type: ORGANELLE OR CELLULAR COMPONENT
Details: Flagellar filament segment complex comprised of 22 FlaB flagellin proteins
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Roseburia hominis (bacteria) / Strain: A2-183 / Cellular location: Bacterial flagellum
Buffer solutionpH: 7.4
Details: PBS buffer was from a stock solution (Gibco #10010031). Formula: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMSodium chlorideNaCl1
22.7 mMPotassium chlorideKCl1
310 mMDisodium phosphateNa2HPO41
41.8 mMMonopotassium phosphateKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The specimens were sheared from wild-type culture, purified with a sucrose gradient, then washed and resuspended in PBS before imaging.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2480

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Processing

EM software
IDNameVersionCategoryDetails
1crYOLO1.8.2particle selectioncrYOLO was used to automatically select helical segments
2EPUimage acquisition
4CTFFIND4.1.13CTF correctionCTFFind4 through Transphire was used to apply Motion correction & CTF correction to extracted segments.
7UCSF ChimeraX1.7model fitting
9ISOLDE1.6model refinement
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.4424 ° / Axial rise/subunit: 4.69 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 576587
Details: Particles were picked automatically using helical picking with crYOLO
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 443605 / Algorithm: FOURIER SPACE / Num. of class averages: 45 / Symmetry type: HELICAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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