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- PDB-8wlt: Cryo-EM structure of the membrane-anchored part of the flagellar ... -

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Basic information

Entry
Database: PDB / ID: 8wlt
TitleCryo-EM structure of the membrane-anchored part of the flagellar motor-hook complex in the CCW state
Components
  • (Flagellar basal-body rod protein ...) x 3
  • (Flagellar biosynthetic protein ...) x 3
  • Flagellar L-ring protein
  • Flagellar M-ring protein
  • Flagellar P-ring protein
  • Flagellar basal body rod protein FlgB
  • Flagellar hook protein FlgE
  • Flagellar hook-basal body complex protein FliE
KeywordsMOTOR PROTEIN / Flagellar motor / Flagellum
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity ...bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / protein secretion / bacterial-type flagellum-dependent cell motility / protein targeting / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity / plasma membrane
Similarity search - Function
Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ ...Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Flagellar basal-body rod protein FlgC / Flagellar hook protein FlgE / Flagellar basal-body rod protein FlgG / Flagellar biosynthetic protein FliQ / Flagellar L-ring protein / Flagellar M-ring protein / Flagellar P-ring protein / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE ...Flagellar basal-body rod protein FlgC / Flagellar hook protein FlgE / Flagellar basal-body rod protein FlgG / Flagellar biosynthetic protein FliQ / Flagellar L-ring protein / Flagellar M-ring protein / Flagellar P-ring protein / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsTan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)U23A20163 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the membrane-anchored part of the flagellar motor-hook complex in the CCW state
Authors: Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
History
DepositionOct 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar L-ring protein
B: Flagellar L-ring protein
C: Flagellar L-ring protein
D: Flagellar L-ring protein
E: Flagellar L-ring protein
F: Flagellar L-ring protein
G: Flagellar L-ring protein
H: Flagellar L-ring protein
I: Flagellar L-ring protein
J: Flagellar L-ring protein
K: Flagellar L-ring protein
L: Flagellar L-ring protein
M: Flagellar L-ring protein
N: Flagellar L-ring protein
O: Flagellar L-ring protein
P: Flagellar L-ring protein
Q: Flagellar L-ring protein
R: Flagellar L-ring protein
S: Flagellar L-ring protein
T: Flagellar L-ring protein
U: Flagellar L-ring protein
V: Flagellar L-ring protein
W: Flagellar L-ring protein
X: Flagellar L-ring protein
Y: Flagellar L-ring protein
Z: Flagellar L-ring protein
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
0: Flagellar basal-body rod protein FlgG
1: Flagellar basal-body rod protein FlgG
2: Flagellar basal-body rod protein FlgG
3: Flagellar basal-body rod protein FlgG
4: Flagellar basal-body rod protein FlgG
5: Flagellar basal-body rod protein FlgG
6: Flagellar basal-body rod protein FlgG
7: Flagellar basal-body rod protein FlgG
8: Flagellar basal-body rod protein FlgG
9: Flagellar basal-body rod protein FlgG
ZA: Flagellar basal-body rod protein FlgG
ZB: Flagellar basal-body rod protein FlgG
ZC: Flagellar basal-body rod protein FlgG
ZD: Flagellar basal-body rod protein FlgG
ZE: Flagellar basal-body rod protein FlgG
ZF: Flagellar hook protein FlgE
ZG: Flagellar hook protein FlgE
ZH: Flagellar hook protein FlgE
ZI: Flagellar hook protein FlgE
ZJ: Flagellar hook protein FlgE
ZK: Flagellar hook protein FlgE
ZL: Flagellar hook protein FlgE
ZM: Flagellar hook protein FlgE
ZN: Flagellar hook protein FlgE
ZO: Flagellar hook protein FlgE
ZP: Flagellar hook protein FlgE
ZQ: Flagellar hook protein FlgE
ZR: Flagellar hook protein FlgE
ZS: Flagellar hook protein FlgE
ZT: Flagellar hook protein FlgE
ZU: Flagellar hook protein FlgE
ZV: Flagellar hook protein FlgE
ZW: Flagellar hook protein FlgE
ZX: Flagellar hook protein FlgE
ZY: Flagellar hook protein FlgE
ZZ: Flagellar hook protein FlgE
Za: Flagellar hook protein FlgE
Zb: Flagellar hook protein FlgE
Zc: Flagellar hook protein FlgE
Zd: Flagellar hook protein FlgE
Ze: Flagellar hook protein FlgE
Zf: Flagellar hook protein FlgE
Zg: Flagellar hook protein FlgE
Zh: Flagellar hook protein FlgE
AA: Flagellar basal-body rod protein FlgF
AB: Flagellar basal-body rod protein FlgF
AC: Flagellar basal-body rod protein FlgF
AD: Flagellar basal-body rod protein FlgF
AE: Flagellar basal-body rod protein FlgF
AF: Flagellar basal-body rod protein FlgG
AG: Flagellar basal-body rod protein FlgG
AH: Flagellar basal-body rod protein FlgG
AI: Flagellar basal-body rod protein FlgG
AJ: Flagellar basal-body rod protein FlgG
AK: Flagellar basal-body rod protein FlgG
AL: Flagellar basal-body rod protein FlgG
AM: Flagellar basal-body rod protein FlgG
AN: Flagellar basal-body rod protein FlgG
AR: Flagellar M-ring protein
AS: Flagellar M-ring protein
AT: Flagellar M-ring protein
AU: Flagellar M-ring protein
AV: Flagellar M-ring protein
AW: Flagellar M-ring protein
AX: Flagellar M-ring protein
AY: Flagellar M-ring protein
AZ: Flagellar M-ring protein
Aa: Flagellar M-ring protein
Ab: Flagellar biosynthetic protein FliQ
Ac: Flagellar M-ring protein
Ad: Flagellar M-ring protein
Ae: Flagellar M-ring protein
Af: Flagellar M-ring protein
Ag: Flagellar M-ring protein
Ah: Flagellar M-ring protein
Ai: Flagellar M-ring protein
Aj: Flagellar M-ring protein
Ak: Flagellar M-ring protein
Al: Flagellar M-ring protein
Am: Flagellar M-ring protein
An: Flagellar M-ring protein
Ao: Flagellar M-ring protein
Ap: Flagellar M-ring protein
AO: Flagellar M-ring protein
AP: Flagellar M-ring protein
AQ: Flagellar M-ring protein
Aq: Flagellar biosynthetic protein FliQ
Ar: Flagellar biosynthetic protein FliQ
As: Flagellar biosynthetic protein FliQ
At: Flagellar biosynthetic protein FliR
Au: Flagellar biosynthetic protein FliP
Av: Flagellar biosynthetic protein FliP
Aw: Flagellar biosynthetic protein FliP
Ax: Flagellar biosynthetic protein FliP
Ay: Flagellar biosynthetic protein FliP
Az: Flagellar hook-basal body complex protein FliE
A1: Flagellar hook-basal body complex protein FliE
A2: Flagellar hook-basal body complex protein FliE
A3: Flagellar hook-basal body complex protein FliE
A4: Flagellar hook-basal body complex protein FliE
A5: Flagellar hook-basal body complex protein FliE
A6: Flagellar basal body rod protein FlgB
A7: Flagellar basal body rod protein FlgB
A8: Flagellar basal body rod protein FlgB
A9: Flagellar basal body rod protein FlgB
A0: Flagellar basal body rod protein FlgB
UI: Flagellar M-ring protein
UJ: Flagellar M-ring protein
UK: Flagellar M-ring protein
UL: Flagellar M-ring protein
UM: Flagellar M-ring protein
UN: Flagellar M-ring protein
UO: Flagellar M-ring protein
UP: Flagellar M-ring protein
BA: Flagellar basal-body rod protein FlgC
BB: Flagellar basal-body rod protein FlgC
WA: Flagellar M-ring protein
WB: Flagellar M-ring protein
WC: Flagellar M-ring protein
WD: Flagellar M-ring protein
WE: Flagellar M-ring protein
WF: Flagellar M-ring protein
WG: Flagellar M-ring protein
WH: Flagellar M-ring protein
WI: Flagellar M-ring protein
WJ: Flagellar M-ring protein
WK: Flagellar M-ring protein
WL: Flagellar M-ring protein
WM: Flagellar M-ring protein
WN: Flagellar M-ring protein
WO: Flagellar M-ring protein
WP: Flagellar M-ring protein
WQ: Flagellar M-ring protein
WR: Flagellar M-ring protein
WS: Flagellar M-ring protein
WT: Flagellar M-ring protein
WU: Flagellar M-ring protein
WV: Flagellar M-ring protein
WW: Flagellar M-ring protein
BC: Flagellar basal-body rod protein FlgC
BD: Flagellar basal-body rod protein FlgC
BE: Flagellar basal-body rod protein FlgC
BF: Flagellar basal-body rod protein FlgC
BG: Flagellar M-ring protein
BH: Flagellar M-ring protein
BI: Flagellar M-ring protein
BJ: Flagellar M-ring protein
BK: Flagellar M-ring protein
BL: Flagellar M-ring protein
BM: Flagellar M-ring protein
BN: Flagellar M-ring protein
BO: Flagellar M-ring protein
BP: Flagellar M-ring protein
BQ: Flagellar M-ring protein
BR: Flagellar M-ring protein
BS: Flagellar M-ring protein
BT: Flagellar M-ring protein
BU: Flagellar M-ring protein
BV: Flagellar M-ring protein
BW: Flagellar M-ring protein
BX: Flagellar M-ring protein


Theoretical massNumber of molelcules
Total (without water)8,744,188213
Polymers8,744,188213
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 168 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

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


Mass: 24726.666 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1N8
#2: 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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P15930
#4: Protein ...
Flagellar hook protein FlgE


Mass: 42233.152 Da / Num. of mol.: 29 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1J1
#6: Protein ...
Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 76 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P15928
#10: 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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P26462
#11: 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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P16437

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Flagellar basal-body rod protein ... , 3 types, 35 molecules 0123456789ZAZBZCZDZEAFAGAHAIAJAKALAMANAAABACADAEBA...

#3: 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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1J3
#5: 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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P16323
#12: 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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1I7

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Flagellar biosynthetic protein ... , 3 types, 10 molecules AbAqArAsAtAuAvAwAxAy

#7: Protein
Flagellar biosynthetic protein FliQ


Mass: 9606.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1L5
#8: Protein Flagellar biosynthetic protein FliR


Mass: 28938.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P54702
#9: Protein
Flagellar biosynthetic protein FliP


Mass: 26801.086 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P54700

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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: C ring-containing flagellar motor-hook complex in the CCW state
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
25 mMethylenediaminetetraacetic acidEDTA1
30.1 % v/voctylphenol ethoxylateTX-1001
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Blot time: 2 Blot force: -15 Wait time: 60 Blot total: 1

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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 / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
2SerialEMimage acquisition
4cryoSPARC4.1.1CTF correction
7UCSF Chimera1.17model fitting
8UCSF ChimeraX1.5model fitting
9Coot0.9.8.7model fitting
11cryoSPARC4.1.1initial Euler assignment
12cryoSPARC4.1.1final Euler assignment
14cryoSPARC4.1.13D reconstruction
15PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 22192 / Details: Particles were manually picked using cryoSPARC
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11858 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
ID 3D fitting-IDSource nameTypeDetailsAccession codeInitial refinement model-ID
11AlphaFoldin silico model
21Otherin silico modelModel-Angelo
31PDBexperimental model7CBL3
41PDBexperimental model7CGO

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