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- PDB-7sn9: Cryo-EM structure of the Sinorhizobium meliloti flagellar filament -

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Basic information

Entry
Database: PDB / ID: 7sn9
TitleCryo-EM structure of the Sinorhizobium meliloti flagellar filament
ComponentsFlagellin A
KeywordsSTRUCTURAL PROTEIN / Bacteria flagellar filament / motility / flagellar polymorphism
Function / homologyFlagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / bacterial-type flagellum / structural molecule activity / extracellular region / Flagellin A
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKreutzberger, M.A.B. / Scharf, B.E. / Egelman, E.H.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510
CitationJournal: Nat Commun / Year: 2022
Title: Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments.
Authors: Mark A B Kreutzberger / Richard C Sobe / Amber B Sauder / Sharanya Chatterjee / Alejandro Peña / Fengbin Wang / Jorge A Giron / Volker Kiessling / Tiago R D Costa / Vincent P Conticello / ...Authors: Mark A B Kreutzberger / Richard C Sobe / Amber B Sauder / Sharanya Chatterjee / Alejandro Peña / Fengbin Wang / Jorge A Giron / Volker Kiessling / Tiago R D Costa / Vincent P Conticello / Gad Frankel / Melissa M Kendall / Birgit E Scharf / Edward H Egelman /
Abstract: Flagellar filaments function as the propellers of the bacterial flagellum and their supercoiling is key to motility. The outer domains on the surface of the filament are non-critical for motility in ...Flagellar filaments function as the propellers of the bacterial flagellum and their supercoiling is key to motility. The outer domains on the surface of the filament are non-critical for motility in many bacteria and their structures and functions are not conserved. Here, we show the atomic cryo-electron microscopy structures for flagellar filaments from enterohemorrhagic Escherichia coli O157:H7, enteropathogenic E. coli O127:H6, Achromobacter, and Sinorhizobium meliloti, where the outer domains dimerize or tetramerize to form either a sheath or a screw-like surface. These dimers are formed by 180° rotations of half of the outer domains. The outer domain sheath (ODS) plays a role in bacterial motility by stabilizing an intermediate waveform and prolonging the tumbling of E. coli cells. Bacteria with these ODS and screw-like flagellar filaments are commonly found in soil and human intestinal environments of relatively high viscosity suggesting a role for the dimerization in these environments.
History
DepositionOct 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Flagellin A
P: Flagellin A
B: Flagellin A
W: Flagellin A
C: Flagellin A
X: Flagellin A
D: Flagellin A
Y: Flagellin A
E: Flagellin A
Z: Flagellin A
F: Flagellin A
a: Flagellin A
G: Flagellin A
b: Flagellin A
H: Flagellin A
c: Flagellin A
I: Flagellin A
d: Flagellin A
J: Flagellin A
e: Flagellin A
K: Flagellin A
f: Flagellin A
L: Flagellin A
g: Flagellin A
M: Flagellin A
h: Flagellin A
N: Flagellin A
i: Flagellin A
O: Flagellin A
j: Flagellin A
Q: Flagellin A
k: Flagellin A
R: Flagellin A
l: Flagellin A
S: Flagellin A
m: Flagellin A
T: Flagellin A
n: Flagellin A
U: Flagellin A
o: Flagellin A
V: Flagellin A
p: Flagellin A


Theoretical massNumber of molelcules
Total (without water)1,705,85942
Polymers1,705,85942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellin A


Mass: 40615.680 Da / Num. of mol.: 42
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: flaA / Production host: Sinorhizobium meliloti (bacteria) / References: UniProt: P13118

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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: Structure of the Sinorhizobium meliloti flagellar filament
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sinorhizobium meliloti (bacteria)
Buffer solutionpH: 7.2
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 222 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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19rc4_4035refinement
PHENIX1.19rc4_4035refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 130.9 ° / Axial rise/subunit: 9.5 Å / Axial symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16158 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 122.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0021120078
ELECTRON MICROSCOPYf_angle_d0.4982163170
ELECTRON MICROSCOPYf_chiral_restr0.036420202
ELECTRON MICROSCOPYf_plane_restr0.002721336
ELECTRON MICROSCOPYf_dihedral_angle_d4.601417262

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