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- PDB-7cgo: Cryo-EM structure of the flagellar motor-hook complex from Salmonella -

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Basic information

Entry
Database: PDB / ID: 7cgo
TitleCryo-EM structure of the flagellar motor-hook complex from Salmonella
Components
  • (Flagellar MS ring ...) x 2
  • (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
  • FlgB-Dc loop
  • FliE helix 1
KeywordsMOTOR PROTEIN / Flagella / Hook-basal body
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal 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, rod / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal 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-dependent cell motility / protein secretion / 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 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 P-ring protein / Flagellar P-ring protein / Flagellar biosynthesis protein FliQ / Flagellar basal-body rod FlgG ...Flagellar L-ring protein / Flagellar L-ring protein / 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 P-ring protein / Flagellar P-ring protein / Flagellar biosynthesis protein FliQ / Flagellar basal-body rod FlgG / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / 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. / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / Flagellar basal-body/hook protein, C-terminal domain / FliP family / Flagellar basal body rod FlgEFG protein C-terminal / Flagella transport protein fliP family signature 2. / 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 typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 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
DepositionJul 1, 2020Deposition 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

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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
CE: Flagellar biosynthetic protein FliR
CA: Flagellar biosynthetic protein FliQ
CB: Flagellar biosynthetic protein FliQ
CC: Flagellar biosynthetic protein FliQ
CD: Flagellar biosynthetic protein FliQ
w: Flagellar biosynthetic protein FliP
x: Flagellar biosynthetic protein FliP
y: Flagellar biosynthetic protein FliP
z: Flagellar biosynthetic protein FliP
CF: Flagellar biosynthetic protein FliP
Da: Flagellar M-ring protein
Db: Flagellar M-ring protein
Dc: Flagellar M-ring protein
Dd: Flagellar M-ring protein
De: Flagellar M-ring protein
Df: Flagellar M-ring protein
Dg: Flagellar M-ring protein
Dh: Flagellar M-ring protein
Di: Flagellar M-ring protein
Dj: Flagellar M-ring protein
Dk: Flagellar M-ring protein
Dl: Flagellar M-ring protein
Dm: Flagellar M-ring protein
Dn: Flagellar M-ring protein
Do: Flagellar M-ring protein
Dp: Flagellar M-ring protein
Dq: Flagellar M-ring protein
Dr: Flagellar M-ring protein
Ds: Flagellar M-ring protein
Dt: Flagellar M-ring protein
Du: Flagellar M-ring protein
Dv: Flagellar M-ring protein
Dw: Flagellar M-ring protein
GA: FlgB-Dc loop
GF: FliE helix 1
GG: FliE helix 1
GH: FliE helix 1
GI: FliE helix 1
GJ: FliE helix 1
GK: FliE helix 1
GC: FlgB-Dc loop
GE: FlgB-Dc loop
GD: FlgB-Dc loop
GB: FlgB-Dc loop
Ca: Flagellar M-ring protein
Cb: Flagellar M-ring protein
Cc: Flagellar M-ring protein
Cd: Flagellar M-ring protein
Ce: Flagellar M-ring protein
Cf: Flagellar M-ring protein
Cg: Flagellar M-ring protein
Ch: Flagellar M-ring protein
Ci: Flagellar M-ring protein
Cj: Flagellar M-ring protein
Ck: Flagellar M-ring protein
Cl: Flagellar M-ring protein
Cm: Flagellar M-ring protein
Cn: Flagellar M-ring protein
Co: Flagellar M-ring protein
Cp: Flagellar M-ring protein
Cq: Flagellar M-ring protein
Cr: Flagellar M-ring protein
Cs: Flagellar M-ring protein
Ct: Flagellar M-ring protein
Cu: Flagellar M-ring protein
Cv: Flagellar M-ring protein
Cw: Flagellar M-ring protein
Cx: Flagellar M-ring protein
Cy: Flagellar M-ring protein
Cz: Flagellar M-ring protein
Ea: Flagellar M-ring protein
Eb: Flagellar M-ring protein
Ec: Flagellar M-ring protein
Ed: Flagellar M-ring protein
Ee: Flagellar M-ring protein
Ef: Flagellar M-ring protein
Eg: Flagellar M-ring protein
Eh: Flagellar M-ring protein
AA: Flagellar L-ring protein
AB: Flagellar L-ring protein
AC: Flagellar L-ring protein
AD: Flagellar L-ring protein
AE: Flagellar L-ring protein
AF: Flagellar L-ring protein
AG: Flagellar L-ring protein
AH: Flagellar L-ring protein
AI: Flagellar L-ring protein
AJ: Flagellar L-ring protein
AK: Flagellar L-ring protein
AL: Flagellar L-ring protein
AM: Flagellar L-ring protein
AN: Flagellar L-ring protein
AO: Flagellar L-ring protein
AP: Flagellar L-ring protein
AQ: Flagellar L-ring protein
AR: Flagellar L-ring protein
AS: Flagellar L-ring protein
AT: Flagellar L-ring protein
AU: Flagellar L-ring protein
AV: Flagellar L-ring protein
AW: Flagellar L-ring protein
AX: Flagellar L-ring protein
AY: Flagellar L-ring protein
AZ: Flagellar L-ring protein
BA: Flagellar P-ring protein
BB: Flagellar P-ring protein
BC: Flagellar P-ring protein
BD: Flagellar P-ring protein
BE: Flagellar P-ring protein
BF: Flagellar P-ring protein
BG: Flagellar P-ring protein
BH: Flagellar P-ring protein
BI: Flagellar P-ring protein
BJ: Flagellar P-ring protein
BK: Flagellar P-ring protein
BL: Flagellar P-ring protein
BM: Flagellar P-ring protein
BN: Flagellar P-ring protein
BO: Flagellar P-ring protein
BP: Flagellar P-ring protein
BQ: Flagellar P-ring protein
BR: Flagellar P-ring protein
BS: Flagellar P-ring protein
BT: Flagellar P-ring protein
BU: Flagellar P-ring protein
BV: Flagellar P-ring protein
BW: Flagellar P-ring protein
BX: Flagellar P-ring protein
BY: Flagellar P-ring protein
BZ: Flagellar P-ring protein
DL: Flagellar hook protein FlgE
DM: Flagellar hook protein FlgE
DN: Flagellar hook protein FlgE
DO: Flagellar hook protein FlgE
DP: Flagellar hook protein FlgE
DQ: Flagellar hook protein FlgE
DR: Flagellar hook protein FlgE
DS: Flagellar hook protein FlgE
DT: Flagellar hook protein FlgE
DU: Flagellar hook protein FlgE
DV: Flagellar hook protein FlgE
DW: Flagellar hook protein FlgE
DX: Flagellar hook protein FlgE
DY: Flagellar hook protein FlgE
DZ: Flagellar hook protein FlgE
EA: Flagellar hook protein FlgE
EB: Flagellar hook protein FlgE
EC: Flagellar hook protein FlgE
ED: Flagellar hook protein FlgE
EE: Flagellar hook protein FlgE
EF: Flagellar hook protein FlgE
EG: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)7,785,661219
Polymers7,785,661219
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 , 6 types, 153 molecules lmoknqrstuvDADBDCDDDEDFDGDHDIDJDKDLDMDNDODPDQDRDS...

#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.: 33 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P0A1J1
#12: Protein ...
Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 57 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P15928
#15: Protein ...
Flagellar L-ring protein / Basal body L-ring protein


Mass: 24965.076 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P0A1N8
#16: 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)
References: UniProt: P15930

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

#9: Protein Flagellar biosynthetic protein FliR


Mass: 28938.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P54702
#10: Protein
Flagellar biosynthetic protein FliQ


Mass: 9606.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P0A1L5
#11: Protein
Flagellar biosynthetic protein FliP


Mass: 26801.086 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P54700

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Protein/peptide , 2 types, 11 molecules GAGCGEGDGBGFGGGHGIGJGK

#13: Protein/peptide
FlgB-Dc loop


Mass: 1039.273 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
#14: Protein/peptide
FliE helix 1


Mass: 1549.902 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Details

Has ligand of interestY
Sequence details1. The full sequence of Flagellar M-ring protein is listed below: ...1. The full sequence of Flagellar M-ring protein is listed below: MSATASTATQPKPLEWLNRLRANPRIPLIVAGSAAVAIVVAMVLWAKTPDYRTLFSNLSDQDGGAIVAQLTQMNIPYRFANGSGAIEVPADKVHELRLRLAQQGLPKGGAVGFELLDQEKFGISQFSEQVNYQRALEGELARTIETLGPVKSARVHLAMPKPSLFVREQKSPSASVTVTLEPGRALDEGQISAVVHLVSSAVAGLPPGNVTLVDQSGHLLTQSNTSGRDLNDAQLKFANDVESRIQRRIEAILSPIVGNGNVHAQVTAQLDFANKEQTEEHYSPNGDASKATLRSRQLNISEQVGAGYPGGVPGALSNQPAPPNEAPIATPPTNQQNAQNTPQTSTSTNSNSAGPRSTQRNETSNYEVDRTIRHTKMNVGDIERLSVAVVVNYKTLADGKPLPLTADQMKQIEDLTREAMGFSDKRGDTLNVVNSPFSAVDNTGGELPFWQQQSFIDQLLAAGRWLLVLVVAWILWRKAVRPQLTRRVEEAKAAQEQAQVRQETEEAVEVRLSKDEQLQQRRANQRLGAEVMSQRIREMSDNDPRVVALVIRQWMSNDHE 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). 2. The full sequence of FlgB is listed below: MLDRLDAALRFQQEALNLRAQRQEILAANIANADTPGYQARDIDFASELKKVMVRGREETGGVALTLTSSHHIPAQAVSSPAVDLLYRVPDQPSLDGNTVDMDRERTQFADNSLKYQMGLTVLGSQLKGMMNVLQGGN The FlgB-Dc loop is a fragment of FlgB, but the residues in chains GA/GB/GC/GD/GE could not be precisely built due to their low densities. The residues of FlgB-Dc loop are likely located between the residues of 56-81 of FlgB according to its relative position. 3. The full sequence of FliE is listed below: MAAIQGIEGVISQLQATAMAARGQDTHSQSTVSFAGQLHAALDRISDRQAAARVQAEKFTLGEPGIALNDVMADMQKASVSMQMGIQVRNKLVAAYQEVMSMQV The FliE-helix 1 is a fragment of FliE, but the residues in chains GF/GG/GH/GI/GJ/GK could not be precisely built due to their low densities. The residues are likely located between the residues of 1-22 of FliE according to its relative posion.

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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 complex / 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 hydrochloride-hydrochlorideTris-HClTris1
25 mMethylene diamine tetraacetic acidEDTAEthylenediaminetetraacetic acid1
30.1 v/v2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanolTritonX-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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52714 / Symmetry type: POINT

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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