[English] 日本語
Yorodumi
- PDB-8fte: CryoEM strucutre of 22-mer RBM2 of the Salmonella MS-ring -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fte
TitleCryoEM strucutre of 22-mer RBM2 of the Salmonella MS-ring
ComponentsFlagellar M-ring protein
KeywordsMOTOR PROTEIN / flagellar / 22-fold / ring-building motif / MS-ring / FliF
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / plasma membrane
Similarity search - Function
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 M-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSingh, P.S. / Nakagawa, T. / Cecchini, G. / Iverson, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)GM61606 United States
CitationJournal: PLoS One / Year: 2023
Title: CryoEM structure of a post-assembly MS-ring reveals plasticity in stoichiometry and conformation.
Authors: Prashant K Singh / Gary Cecchini / Terunaga Nakagawa / T M Iverson /
Abstract: The flagellar motor supports bacterial chemotaxis, a process that allows bacteria to move in response to their environment. A central feature of this motor is the MS-ring, which is composed entirely ...The flagellar motor supports bacterial chemotaxis, a process that allows bacteria to move in response to their environment. A central feature of this motor is the MS-ring, which is composed entirely of repeats of the FliF subunit. This MS-ring is critical for the assembly and stability of the flagellar switch and the entire flagellum. Despite multiple independent cryoEM structures of the MS-ring, there remains a debate about the stoichiometry and organization of the ring-building motifs (RBMs). Here, we report the cryoEM structure of a Salmonella MS-ring that was purified from the assembled flagellar switch complex (MSC-ring). We term this the 'post-assembly' state. Using 2D class averages, we show that under these conditions, the post-assembly MS-ring can contain 32, 33, or 34 FliF subunits, with 33 being the most common. RBM3 has a single location with C32, C33, or C34 symmetry. RBM2 is found in two locations with RBM2inner having C21 or C22 symmetry and an RBM2outer-RBM1 having C11 symmetry. Comparison to previously reported structures identifies several differences. Most strikingly, we find that the membrane domain forms 11 regions of discrete density at the base of the structure rather than a contiguous ring, although density could not be unambiguously interpreted. We further find density in some previously unresolved areas, and we assigned amino acids to those regions. Finally, we find differences in interdomain angles in RBM3 that affect the diameter of the ring. Together, these investigations support a model of the flagellum with structural plasticity, which may be important for flagellar assembly and function.
History
DepositionJan 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar M-ring protein
B: Flagellar M-ring protein
C: Flagellar M-ring protein
D: Flagellar M-ring protein
E: Flagellar M-ring protein
F: Flagellar M-ring protein
G: Flagellar M-ring protein
H: Flagellar M-ring protein
I: Flagellar M-ring protein
J: Flagellar M-ring protein
K: Flagellar M-ring protein
L: Flagellar M-ring protein
M: Flagellar M-ring protein
N: Flagellar M-ring protein
O: Flagellar M-ring protein
P: Flagellar M-ring protein
Q: Flagellar M-ring protein
R: Flagellar M-ring protein
S: Flagellar M-ring protein
T: Flagellar M-ring protein
V: Flagellar M-ring protein
W: Flagellar M-ring protein


Theoretical massNumber of molelcules
Total (without water)1,348,50422
Polymers1,348,50422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "W"
d_2ens_1chain "B"
d_3ens_1chain "R"
d_4ens_1chain "D"
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 "A"
d_16ens_1chain "P"
d_17ens_1chain "C"
d_18ens_1chain "O"
d_19ens_1chain "S"
d_20ens_1chain "T"
d_21ens_1chain "V"
d_22ens_1chain "Q"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 125 - 227 / Label seq-ID: 125 - 227

Dom-IDAuth asym-IDLabel asym-ID
d_1WV
d_2BB
d_3RR
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ
d_11KK
d_12LL
d_13MM
d_14NN
d_15AA
d_16PP
d_17CC
d_18OO
d_19SS
d_20TT
d_21VU
d_22QQ

-
Components

#1: Protein ...
Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliF, fla AII.1, fla BI, STM1969 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15928

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: MS-ring of the flagellar complex / Type: COMPLEX
Details: CryoEM strucutre of the 22-mer RBM2 region of the Salmonella MS-ring
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Details: 50 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.1 % Ana-grade LDAO
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCl1
2100 mMSodium ChlorideNaCl1
30.1 Percentn-Dodecyl-N,N-Dimethylamine-N-Oxide (LDAO)1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GRAPHENE OXIDE / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Purified MS-rings were added to each grid at 277.15K at 100% humidity. After 30 sec of incubation, blotting was performed for 12 sec. The grid was then plunged into liquid ethane using a ...Details: Purified MS-rings were added to each grid at 277.15K at 100% humidity. After 30 sec of incubation, blotting was performed for 12 sec. The grid was then plunged into liquid ethane using a Vitrobot Mark IV system (Thermo Fisher)

-
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 defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
1cryoSPARC2.15particle selection
4cryoSPARC2.15CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC2.15initial Euler assignment
10cryoSPARC2.15final Euler assignment
12cryoSPARC4.0.13D reconstruction
13PHENIX1.20.1model refinement
14Coot0.9.8.4model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C22 (22 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100096 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 141.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004715092
ELECTRON MICROSCOPYf_angle_d0.968620570
ELECTRON MICROSCOPYf_chiral_restr0.04872552
ELECTRON MICROSCOPYf_plane_restr0.00982706
ELECTRON MICROSCOPYf_dihedral_angle_d17.31335456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2VELECTRON MICROSCOPYNCS constraints9.47726389381E-13
ens_1d_3VELECTRON MICROSCOPYNCS constraints2.72696213631E-11
ens_1d_4VELECTRON MICROSCOPYNCS constraints2.75770789756E-13
ens_1d_5VELECTRON MICROSCOPYNCS constraints2.9281914433E-13
ens_1d_6VELECTRON MICROSCOPYNCS constraints1.2886965728E-12
ens_1d_7VELECTRON MICROSCOPYNCS constraints1.46956087487E-10
ens_1d_8VELECTRON MICROSCOPYNCS constraints7.34536635213E-12
ens_1d_9VELECTRON MICROSCOPYNCS constraints5.51047024712E-13
ens_1d_10VELECTRON MICROSCOPYNCS constraints3.9244064881E-11
ens_1d_11VELECTRON MICROSCOPYNCS constraints6.43345457755E-13
ens_1d_12VELECTRON MICROSCOPYNCS constraints2.70810981296E-13
ens_1d_13VELECTRON MICROSCOPYNCS constraints1.54391966126E-11
ens_1d_14VELECTRON MICROSCOPYNCS constraints5.32460712635E-12
ens_1d_15VELECTRON MICROSCOPYNCS constraints3.16028171077E-11
ens_1d_16VELECTRON MICROSCOPYNCS constraints3.23238140619E-12
ens_1d_17VELECTRON MICROSCOPYNCS constraints1.96665314782E-10
ens_1d_18VELECTRON MICROSCOPYNCS constraints2.27902346163E-11
ens_1d_19VELECTRON MICROSCOPYNCS constraints9.63420546603E-12
ens_1d_20VELECTRON MICROSCOPYNCS constraints2.2891090485E-11
ens_1d_21VELECTRON MICROSCOPYNCS constraints2.50170955355E-13
ens_1d_22VELECTRON MICROSCOPYNCS constraints3.01132209323E-11

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more