[English] 日本語
Yorodumi
- PDB-9iyc: P ring on polyrod-P ring complex from Salmonella TH26292 strain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iyc
TitleP ring on polyrod-P ring complex from Salmonella TH26292 strain
ComponentsFlagellar P-ring protein
KeywordsMOTOR PROTEIN / flagella motor. P ring on polyrod(PaPR) complex / Cryo-EM / SPA / Salmonella
Function / homologybacterial-type flagellum basal body, distal rod, P ring / Flagellar P-ring protein / Flagellar P-ring protein / bacterial-type flagellum-dependent cell motility / outer membrane-bounded periplasmic space / structural molecule activity / Flagellar P-ring protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsYamaguchi, T. / Kato, T. / Minamino, T. / Namba, K.
Funding support Japan, 9items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP25000013MEXT KAKENHI Grant Number JP15H01640,JP20H05532 Japan
Japan Society for the Promotion of Science (JSPS)JP18K06155 Japan
Japan Society for the Promotion of Science (JSPS)JP26293097 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03182 Japan
Japan Society for the Promotion of Science (JSPS)JP15H01640 Japan
Japan Society for the Promotion of Science (JSPS)Japan Society for the Promotion of Science (JSPS) Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Society for the Promotion of Science (JSPS)JP21J12128 Japan
CitationJournal: To Be Published
Title: Structural insights into the assembly mechanism of the molecular bushing in the bacterial flagellar motor
Authors: Yamaguchi, T. / Kato, T. / Minamino, T. / Namba, K.
History
DepositionJul 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)943,79526
Polymers943,79526
Non-polymers00
Water00
1


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

-
Components

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


Mass: 36299.820 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: HK26292 / Gene: flgI, fla FIX, flaM, STM1181
Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain (production host): HK26292 / References: UniProt: P15930
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: P ring on polyrod-P ring complex from Salmonella typhimurium HK26292 mutant
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.38 kDa/nm / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Source (recombinant)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(hydroxymethyl)aminomethaneTris-HCl1
250 mMSodum ChlorideNaCl1
325 mMImidazoleImidazole1
40.002 %Lauryl maltose neopentyl glycolLMNG1
50.05 %Triton X-100Triton1
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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: BLOTTING TIME OF 4 SECONDS, 1 SECONDS DRAIN TIME, FORCE 0

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 2000 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector modelNum. of grids imaged
11675GATAN K3 (6k x 4k)1
212.540GATAN K3 (6k x 4k)1

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2.0particle selection
4cryoSPARC3.2.0CTF correction
7PHENIX1.21-rcmodel fitting
9PHENIX1.21-rcmodel refinement
12cryoSPARC3.2.0classification
13RELION3.1.13D reconstruction
Image processing
IDImage recording-ID
11
22
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 386473
SymmetryPoint symmetry: C26 (26 fold cyclic)
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85463 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: Phenix1.21-rc1 , refmac servalcat, coot and ISOLDE was used for fitting, and Phenix was used for final fitting.
Atomic model buildingPDB-ID: 7CLR

7clr


Accession code: 7CLR / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.33 Å

+
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