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- PDB-7e82: Cryo-EM structure of the flagellar rod with partial hook from Sal... -

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Basic information

Entry
Database: PDB / ID: 7.0E+82
TitleCryo-EM structure of the flagellar rod with partial hook from Salmonella
Components
  • (Flagellar MS ring ...) x 2
  • (Flagellar basal-body rod protein ...) x 3
  • Flagellar basal body rod protein FlgB
  • Flagellar hook protein FlgE
  • Flagellar hook-basal body complex protein FliE
KeywordsMOTOR PROTEIN / Flagella / Rod
Function / homology
Function and homology information


bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / structural molecule activity / plasma membrane
Similarity search - Function
Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod FlgG / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G ...Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod FlgG / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar basal-body rod protein FlgC / Flagellar hook protein FlgE / Flagellar basal-body rod protein FlgG / Flagellar M-ring protein / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTan, J.X. / Chang, S.H. / Wang, X.F. / Xu, C.H. / Zhou, Y. / Zhang, X. / Zhu, Y.Q.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504803 China
Ministry of Science and Technology (MoST, China)2018YFA0507700 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)81530068 China
National Natural Science Foundation of China (NSFC)81501717 China
CitationJournal: Cell / Year: 2021
Title: Structural basis of assembly and torque transmission of the bacterial flagellar motor.
Authors: Jiaxing Tan / Xing Zhang / Xiaofei Wang / Caihuang Xu / Shenghai Chang / Hangjun Wu / Ting Wang / Huihui Liang / Haichun Gao / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key ...The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key determinant of pathogenicity. The detailed structure of the flagellar motor remains unknown. Here we present an atomic-resolution cryoelectron microscopy (cryo-EM) structure of the bacterial flagellar motor complexed with the hook, consisting of 175 subunits with a molecular mass of approximately 6.3 MDa. The structure reveals that 10 peptides protruding from the MS ring with the FlgB and FliE subunits mediate torque transmission from the MS ring to the rod and overcome the symmetry mismatch between the rotational and helical structures in the motor. The LP ring contacts the distal rod and applies electrostatic forces to support its rotation and torque transmission to the hook. This work provides detailed molecular insights into the structure, assembly, and torque transmission mechanisms of the flagellar motor.
History
DepositionFeb 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 26, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 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: Flagellar basal-body rod protein FlgG
B: Flagellar basal-body rod protein FlgG
C: Flagellar basal-body rod protein FlgG
D: Flagellar basal-body rod protein FlgG
E: Flagellar basal-body rod protein FlgG
F: Flagellar basal-body rod protein FlgG
G: Flagellar basal-body rod protein FlgG
H: Flagellar basal-body rod protein FlgG
I: Flagellar basal-body rod protein FlgG
J: Flagellar basal-body rod protein FlgG
K: Flagellar basal-body rod protein FlgG
L: Flagellar basal-body rod protein FlgG
M: Flagellar basal-body rod protein FlgG
N: Flagellar basal-body rod protein FlgG
O: Flagellar basal-body rod protein FlgG
P: Flagellar basal-body rod protein FlgG
Q: Flagellar basal-body rod protein FlgG
R: Flagellar basal-body rod protein FlgG
S: Flagellar basal-body rod protein FlgG
T: Flagellar basal-body rod protein FlgG
U: Flagellar basal-body rod protein FlgG
a: Flagellar basal-body rod protein FlgF
b: Flagellar basal-body rod protein FlgF
c: Flagellar basal-body rod protein FlgF
d: Flagellar basal-body rod protein FlgF
e: Flagellar basal-body rod protein FlgF
0: Flagellar MS ring L2
1: Flagellar MS ring L2
2: Flagellar MS ring L2
3: Flagellar MS ring L2
4: Flagellar MS ring L2
5: Flagellar MS ring L1
6: Flagellar MS ring L1
7: Flagellar MS ring L1
9: Flagellar MS ring L1
f: Flagellar basal-body rod protein FlgC
g: Flagellar basal-body rod protein FlgC
h: Flagellar basal-body rod protein FlgC
j: Flagellar basal-body rod protein FlgC
l: Flagellar basal body rod protein FlgB
m: Flagellar basal body rod protein FlgB
o: Flagellar basal body rod protein FlgB
p: Flagellar basal-body rod protein FlgC
8: Flagellar MS ring L1
i: Flagellar basal-body rod protein FlgC
k: Flagellar basal body rod protein FlgB
n: Flagellar basal body rod protein FlgB
V: Flagellar basal-body rod protein FlgG
W: Flagellar basal-body rod protein FlgG
X: Flagellar basal-body rod protein FlgG
q: Flagellar hook-basal body complex protein FliE
r: Flagellar hook-basal body complex protein FliE
s: Flagellar hook-basal body complex protein FliE
t: Flagellar hook-basal body complex protein FliE
u: Flagellar hook-basal body complex protein FliE
v: Flagellar hook-basal body complex protein FliE
DA: Flagellar hook protein FlgE
DB: Flagellar hook protein FlgE
DC: Flagellar hook protein FlgE
DD: Flagellar hook protein FlgE
DE: Flagellar hook protein FlgE
DF: Flagellar hook protein FlgE
DG: Flagellar hook protein FlgE
DH: Flagellar hook protein FlgE
DI: Flagellar hook protein FlgE
DJ: Flagellar hook protein FlgE
DK: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)1,504,67367
Polymers1,504,67367
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Flagellar basal-body rod protein ... , 3 types, 35 molecules ABCDEFGHIJKLMNOPQRSTUVWXabcdef...

#1: Protein ...
Flagellar basal-body rod protein FlgG / Distal rod protein


Mass: 27784.807 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P0A1J3
#2: Protein
Flagellar basal-body rod protein FlgF / Putative proximal rod protein


Mass: 26121.223 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P16323
#5: Protein
Flagellar basal-body rod protein FlgC / Putative proximal rod protein


Mass: 13991.889 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P0A1I7

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Flagellar MS ring ... , 2 types, 10 molecules 0123456798

#3: Protein/peptide
Flagellar MS ring L2


Mass: 1294.587 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
#4: Protein/peptide
Flagellar MS ring L1


Mass: 1998.195 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P15928

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Protein , 3 types, 22 molecules lmoknqrstuvDADBDCDDDEDFDGDHDIDJDK

#6: Protein
Flagellar basal body rod protein FlgB / Putative proximal rod protein


Mass: 15145.061 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P16437
#7: Protein
Flagellar hook-basal body complex protein FliE


Mass: 11087.662 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P26462
#8: Protein
Flagellar hook protein FlgE


Mass: 42233.152 Da / Num. of mol.: 11 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P0A1J1

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Details

Sequence detailsThe complex was purified from the natural source and the sequence of Flagellar M-ring protein is ...The complex was purified from the natural source and the sequence of Flagellar M-ring protein is listed below: MSATASTATQPKPLEWLNRLRANPRIPLIVAGSAAVAIVVAMVLWAKTPDYRTLFSNLSD QDGGAIVAQLTQMNIPYRFANGSGAIEVPADKVHELRLRLAQQGLPKGGAVGFELLDQEK FGISQFSEQVNYQRALEGELARTIETLGPVKSARVHLAMPKPSLFVREQKSPSASVTVTL EPGRALDEGQISAVVHLVSSAVAGLPPGNVTLVDQSGHLLTQSNTSGRDLNDAQLKFAND VESRIQRRIEAILSPIVGNGNVHAQVTAQLDFANKEQTEEHYSPNGDASKATLRSRQLNI SEQVGAGYPGGVPGALSNQPAPPNEAPIATPPTNQQNAQNTPQTSTSTNSNSAGPRSTQR NETSNYEVDRTIRHTKMNVGDIERLSVAVVVNYKTLADGKPLPLTADQMKQIEDLTREAM GFSDKRGDTLNVVNSPFSAVDNTGGELPFWQQQSFIDQLLAAGRWLLVLVVAWILWRKAV RPQLTRRVEEAKAAQEQAQVRQETEEAVEVRLSKDEQLQQRRANQRLGAEVMSQRIREMS DNDPRVVALVIRQWMSNDHE. Residues 311-331 (chains 5/6/7/8/9) could be precisely identified. But the residues in chains 0/1/2/3/4 could not be precisely built due to their low densities, and the model of L2 was built as UNK. The fragment likely contains the residues 'TNQQNAQNTPQTSTS' (333-347) according to its relative position to other fragment (residues 311-331).

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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 motor-hook / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane hydrochloride-hydrochlorideTris-HClTris1
25 mMethylene diamine tetraacetic acidEDTAEthylenediaminetetraacetic acid1
30.1 %octylphenol ethoxylateTX-1001
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: blot for 6 seconds before plunging

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102044 / Symmetry type: POINT

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