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- PDB-7bhq: In situ assembled Salmonella FlgD hook cap complex -

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Basic information

Entry
Database: PDB / ID: 7bhq
TitleIn situ assembled Salmonella FlgD hook cap complex
ComponentsBasal-body rod modification protein FlgD
KeywordsMEMBRANE PROTEIN / bacterial flagellum hook cap salmonella flagellar assembly
Function / homologyFlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / bacterial-type flagellum organization / bacterial-type flagellum-dependent swarming motility / Basal-body rod modification protein FlgD
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJohnson, S. / Furlong, E. / Lea, S.M.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust219477 United Kingdom
Wellcome Trust209194 United Kingdom
Wellcome Trust201536 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
CitationJournal: Nat Microbiol / Year: 2021
Title: Molecular structure of the intact bacterial flagellar basal body.
Authors: Steven Johnson / Emily J Furlong / Justin C Deme / Ashley L Nord / Joseph J E Caesar / Fabienne F V Chevance / Richard M Berry / Kelly T Hughes / Susan M Lea /
Abstract: The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the ...The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids. Here, we present structures of the intact Salmonella flagellar basal body, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2-3.7 Å. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine.
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Basal-body rod modification protein FlgD
B: Basal-body rod modification protein FlgD
C: Basal-body rod modification protein FlgD
D: Basal-body rod modification protein FlgD
E: Basal-body rod modification protein FlgD


Theoretical massNumber of molelcules
Total (without water)120,0085
Polymers120,0085
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area14240 Å2
ΔGint-87 kcal/mol
Surface area48390 Å2

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Components

#1: Protein
Basal-body rod modification protein FlgD


Mass: 24001.637 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: FlgD
Source: (natural) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
References: UniProt: P0A1I9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Flagellar FlgD hook cap complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19rc5_4047refinement
PHENIX1.19rc5_4047refinement
EM software
IDNameVersionCategory
1SIMPLE3particle selection
4SIMPLE3CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29748 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 2145.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00287482
ELECTRON MICROSCOPYf_angle_d0.467810213
ELECTRON MICROSCOPYf_chiral_restr0.04021294
ELECTRON MICROSCOPYf_plane_restr0.00331337
ELECTRON MICROSCOPYf_dihedral_angle_d4.3861040

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