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- PDB-9hmf: Periplasmic scaffold of the Campylobacter jejuni flagellar motor ... -

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Basic information

Entry
Database: PDB / ID: 9hmf
TitlePeriplasmic scaffold of the Campylobacter jejuni flagellar motor (alpha carbon trace)
Components
  • Chemotaxis protein MotB, putative
  • Flagellar protein FliL
  • Lipoprotein, putative
  • PDZ domain-containing protein
  • Paralyzed flagella protein PflA
  • TPR domain protein
KeywordsSTRUCTURAL PROTEIN / molecular machines / flagellar motor / molecular evolution / in situ / scaffold / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / chemotaxis / membrane / plasma membrane
Similarity search - Function
Flagellar protein FlgP / FlgT, N-terminal domain superfamily / Flagellar basal body-associated protein FliL / Flagellar basal body-associated protein FliL / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / PDZ domain / PDZ domain 6 / : / OmpA-like domain profile. ...Flagellar protein FlgP / FlgT, N-terminal domain superfamily / Flagellar basal body-associated protein FliL / Flagellar basal body-associated protein FliL / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / PDZ domain / PDZ domain 6 / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / PDZ domain / OmpA-like domain / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Paralyzed flagella protein PflA / Chemotaxis protein MotB, putative / Lipoprotein, putative / Flagellar protein FliL / TPR domain protein / PDZ domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsDrobnic, T. / Beeby, M.
Funding support United Kingdom, France, United States, 7items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011178/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V000799/1 United Kingdom
Human Frontier Science Program (HFSP)RGP0028/2021-HOCHBERG France
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI065539 United States
Cancer Research UKFC001143 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
CitationJournal: bioRxiv / Year: 2024
Title: Molecular model of a bacterial flagellar motor reveals a "parts-list" of protein adaptations to increase torque.
Authors: Tina Drobnič / Eli J Cohen / Tom Calcraft / Mona Alzheimer / Kathrin Froschauer / Sarah Svensson / William H Hoffmann / Nanki Singh / Sriram G Garg / Louie Henderson / Trishant R Umrekar / ...Authors: Tina Drobnič / Eli J Cohen / Tom Calcraft / Mona Alzheimer / Kathrin Froschauer / Sarah Svensson / William H Hoffmann / Nanki Singh / Sriram G Garg / Louie Henderson / Trishant R Umrekar / Andrea Nans / Deborah Ribardo / Francesco Pedaci / Ashley L Nord / Georg K A Hochberg / David R Hendrixson / Cynthia M Sharma / Peter B Rosenthal / Morgan Beeby /
Abstract: One hurdle to understanding how molecular machines work, and how they evolve, is our inability to see their structures . Here we describe a minicell system that enables cryogenic electron microscopy ...One hurdle to understanding how molecular machines work, and how they evolve, is our inability to see their structures . Here we describe a minicell system that enables cryogenic electron microscopy imaging and single particle analysis to investigate the structure of an iconic molecular machine, the bacterial flagellar motor, which spins a helical propeller for propulsion. We determine the structure of the high-torque motor including the subnanometre-resolution structure of the periplasmic scaffold, an adaptation essential to high torque. Our structure enables identification of new proteins, and interpretation with molecular models highlights origins of new components, reveals modifications of the conserved motor core, and explain how these structures both template a wider ring of motor proteins, and buttress the motor during swimming reversals. We also acquire insights into universal principles of flagellar torque generation. This approach is broadly applicable to other membrane-residing bacterial molecular machines complexes.
History
DepositionDec 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Flagellar protein FliL
P: Flagellar protein FliL
Q: Flagellar protein FliL
R: Flagellar protein FliL
K: Paralyzed flagella protein PflA
L: TPR domain protein
D: PDZ domain-containing protein
E: PDZ domain-containing protein
F: PDZ domain-containing protein
G: PDZ domain-containing protein
H: PDZ domain-containing protein
I: PDZ domain-containing protein
J: PDZ domain-containing protein
C: Lipoprotein, putative
B: Lipoprotein, putative
A: Lipoprotein, putative
M: Chemotaxis protein MotB, putative
N: Chemotaxis protein MotB, putative


Theoretical massNumber of molelcules
Total (without water)665,69118
Polymers665,69118
Non-polymers00
Water00
1
O: Flagellar protein FliL
P: Flagellar protein FliL
Q: Flagellar protein FliL
R: Flagellar protein FliL
K: Paralyzed flagella protein PflA
L: TPR domain protein
D: PDZ domain-containing protein
E: PDZ domain-containing protein
F: PDZ domain-containing protein
G: PDZ domain-containing protein
H: PDZ domain-containing protein
I: PDZ domain-containing protein
J: PDZ domain-containing protein
C: Lipoprotein, putative
B: Lipoprotein, putative
A: Lipoprotein, putative
M: Chemotaxis protein MotB, putative
N: Chemotaxis protein MotB, putative
x 17


Theoretical massNumber of molelcules
Total (without water)11,316,751306
Polymers11,316,751306
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation16

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Components

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Protein , 6 types, 18 molecules OPQRKLDEFGHIJCBAMN

#1: Protein
Flagellar protein FliL / Coordinate model: Cα atoms only


Mass: 19902.945 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / References: UniProt: A0A0H3PIF6
#2: Protein Paralyzed flagella protein PflA / Coordinate model: Cα atoms only


Mass: 91084.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / References: UniProt: A0A0H3PAU5
#3: Protein TPR domain protein / Coordinate model: Cα atoms only


Mass: 93534.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / References: UniProt: A0A0H3PJ87
#4: Protein
PDZ domain-containing protein / Coordinate model: Cα atoms only


Mass: 41455.691 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / References: UniProt: A0A1E7NUR8
#5: Protein Lipoprotein, putative / Coordinate model: Cα atoms only


Mass: 18545.180 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / References: UniProt: A0A0H3PCP8
#6: Protein Chemotaxis protein MotB, putative / Coordinate model: Cα atoms only (Chain-M)


Mass: 27817.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / References: UniProt: A0A0H3PBX6

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Details

Has protein modificationN

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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: Periplasmic scaffold structures of the Campylobacter jejuni flagellar motor
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Campylobacter jejuni (Campylobacter) / Strain: 81-176
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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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 defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector model
111750GATAN K2 SUMMIT (4k x 4k)
2150FEI FALCON III (4k x 4k)
Image scans
Movie frames/imageIDImage recording-IDEntry-ID
32119HMF
229HMF

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3.1.1particle selectionmanual
2EPUimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C17 (17 fold cyclic)
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32790 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building
ID 3D fitting-IDChain-IDSource nameType
11AAlphaFoldin silico model
21BAlphaFoldin silico model
31CAlphaFoldin silico model
41DAlphaFoldin silico model
51EAlphaFoldin silico model
61FAlphaFoldin silico model
71GAlphaFoldin silico model
81HAlphaFoldin silico model
91IAlphaFoldin silico model
101JAlphaFoldin silico model
111KAlphaFoldin silico model
121LAlphaFoldin silico model
131MAlphaFoldin silico model
141NAlphaFoldin silico model
151OSwissModelin silico model
161PSwissModelin silico model
171QSwissModelin silico model
181RSwissModelin silico model

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