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- PDB-7bj2: Salmonella flagellar basal body assembly intermediate - P ring al... -

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Basic information

Entry
Database: PDB / ID: 7bj2
TitleSalmonella flagellar basal body assembly intermediate - P ring alone structure
ComponentsFlagellar P-ring protein
KeywordsPROTEIN TRANSPORT / bacterial flagellum rod bacterial flagellum export gate basal body
Function / homologybacterial-type flagellum basal body, distal rod, P ring / Flagellar P-ring protein / Flagellar P-ring protein / bacterial-type flagellum-dependent cell motility / outer membrane-bounded periplasmic space / structural molecule activity / Flagellar P-ring protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 13, 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

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
a: Flagellar P-ring protein
b: Flagellar P-ring protein
c: Flagellar P-ring protein
d: Flagellar P-ring protein
e: Flagellar P-ring protein
f: Flagellar P-ring protein
g: Flagellar P-ring protein
h: Flagellar P-ring protein
i: Flagellar P-ring protein
j: Flagellar P-ring protein
k: Flagellar P-ring protein
l: Flagellar P-ring protein
m: Flagellar P-ring protein
n: Flagellar P-ring protein
o: Flagellar P-ring protein
p: Flagellar P-ring protein
q: Flagellar P-ring protein
r: Flagellar P-ring protein
s: Flagellar P-ring protein
t: Flagellar P-ring protein
u: Flagellar P-ring protein
v: Flagellar P-ring protein
w: Flagellar P-ring protein
x: Flagellar P-ring protein
y: Flagellar P-ring protein
z: Flagellar P-ring protein


Theoretical massNumber of molelcules
Total (without water)993,04926
Polymers993,04926
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "d"
d_2ens_1chain "p"
d_3ens_1chain "c"
d_4ens_1chain "b"
d_5ens_1chain "e"
d_6ens_1chain "f"
d_7ens_1chain "g"
d_8ens_1chain "h"
d_9ens_1chain "i"
d_10ens_1chain "j"
d_11ens_1chain "k"
d_12ens_1chain "l"
d_13ens_1chain "m"
d_14ens_1chain "n"
d_15ens_1chain "o"
d_16ens_1chain "a"
d_17ens_1chain "q"
d_18ens_1chain "r"
d_19ens_1chain "s"
d_20ens_1chain "t"
d_21ens_1chain "u"
d_22ens_1chain "v"
d_23ens_1chain "w"
d_24ens_1chain "x"
d_25ens_1chain "y"
d_26ens_1chain "z"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUILED1 - 306
d_21ens_1GLUILEP1 - 306
d_31ens_1GLUILEC1 - 306
d_41ens_1GLUILEB1 - 306
d_51ens_1GLUILEE1 - 306
d_61ens_1GLUILEF1 - 306
d_71ens_1GLUILEG1 - 306
d_81ens_1GLUILEH1 - 306
d_91ens_1GLUILEI1 - 306
d_101ens_1GLUILEJ1 - 306
d_111ens_1GLUILEK1 - 306
d_121ens_1GLUILEL1 - 306
d_131ens_1GLUILEM1 - 306
d_141ens_1GLUILEN1 - 306
d_151ens_1GLUILEO1 - 306
d_161ens_1GLUILEA1 - 306
d_171ens_1GLUILEQ1 - 306
d_181ens_1GLUILER1 - 306
d_191ens_1GLUILES1 - 306
d_201ens_1GLUILET1 - 306
d_211ens_1GLUILEU1 - 306
d_221ens_1GLUILEV1 - 306
d_231ens_1GLUILEW1 - 306
d_241ens_1GLUILEX1 - 306
d_251ens_1GLUILEY1 - 306
d_261ens_1GLUILEZ1 - 306

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Components

#1: Protein ...
Flagellar P-ring protein / Basal body P-ring protein


Mass: 38194.176 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P15930

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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 P ring assembly intermediate / Type: COMPLEX / Entity ID: #1 / 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 FIELDBright-field microscopy
Image recordingElectron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19rc5_4047refinement
PHENIX1.19rc5_4047refinement
EM software
IDNameVersionCategory
4SIMPLE3CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C26 (26回回転対称)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58474 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002958942
ELECTRON MICROSCOPYf_angle_d0.577679950
ELECTRON MICROSCOPYf_chiral_restr0.04419932
ELECTRON MICROSCOPYf_plane_restr0.004110582
ELECTRON MICROSCOPYf_dihedral_angle_d4.69638450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefinement-IDTypeRms dev position (Å)
ens_1d_2pELECTRON MICROSCOPYNCS constraints0.000702849801291
ens_1d_3cELECTRON MICROSCOPYNCS constraints0.066977679478
ens_1d_4bELECTRON MICROSCOPYNCS constraints0.000725527538449
ens_1d_5eELECTRON MICROSCOPYNCS constraints0.000712465553422
ens_1d_6fELECTRON MICROSCOPYNCS constraints0.000713036571994
ens_1d_7gELECTRON MICROSCOPYNCS constraints0.000698384774126
ens_1d_8hELECTRON MICROSCOPYNCS constraints0.000697054833726
ens_1d_9iELECTRON MICROSCOPYNCS constraints0.000702772928358
ens_1d_10jELECTRON MICROSCOPYNCS constraints0.000693679989968
ens_1d_11kELECTRON MICROSCOPYNCS constraints0.000714326022886
ens_1d_12lELECTRON MICROSCOPYNCS constraints0.000701738974767
ens_1d_13mELECTRON MICROSCOPYNCS constraints0.000699448773899
ens_1d_14nELECTRON MICROSCOPYNCS constraints0.000711809573125
ens_1d_15oELECTRON MICROSCOPYNCS constraints0.000704408179964
ens_1d_16oELECTRON MICROSCOPYNCS constraints0.000707142619822
ens_1d_17aELECTRON MICROSCOPYNCS constraints0.000714395588658
ens_1d_18qELECTRON MICROSCOPYNCS constraints0.000710872953667
ens_1d_19rELECTRON MICROSCOPYNCS constraints0.000709044624133
ens_1d_20sELECTRON MICROSCOPYNCS constraints0.000707130748771
ens_1d_21tELECTRON MICROSCOPYNCS constraints0.000712955253482
ens_1d_22uELECTRON MICROSCOPYNCS constraints0.0669565852029
ens_1d_23vELECTRON MICROSCOPYNCS constraints0.0947221597582
ens_1d_24wELECTRON MICROSCOPYNCS constraints0.0669761416152
ens_1d_25xELECTRON MICROSCOPYNCS constraints0.0669984912706
ens_1d_26yELECTRON MICROSCOPYNCS constraints0.000701755495072

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