[English] 日本語
Yorodumi
- PDB-9k29: Structure of the Salmonella flagellar FliPQR complex reconstitute... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k29
TitleStructure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc
Components
  • Flagellar biosynthetic protein FliP
  • Flagellar biosynthetic protein FliQ
  • Flagellar biosynthetic protein FliR
KeywordsPROTEIN TRANSPORT / Bacterial flagellum / flagellar assembly / electron Cryomicroscopy / type III secretion system / Salmonella / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / protein secretion / protein targeting / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FliQ / Flagellar transport protein FliP / Flagellar biosynthesis protein FliR / Bacterial export protein family 3 / 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. / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1
Similarity search - Domain/homology
Flagellar biosynthetic protein FliQ / 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: 3 Å
AuthorsKinoshita, M. / Miyata, T. / Makino, F. / Imada, K. / Namba, K. / Minamino, T.
Funding support Japan, 10items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20K15749 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06162 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03182 Japan
Japan Society for the Promotion of Science (JSPS)JP22H02573 Japan
Japan Society for the Promotion of Science (JSPS)JP22K19274 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP20H05532 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H04844 Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: A β-cap on the FliPQR protein-export channel acts as the cap for initial flagellar rod assembly.
Authors: Miki Kinoshita / Tomoko Miyata / Fumiaki Makino / Katsumi Imada / Keiichi Namba / Tohru Minamino /
Abstract: The FliPQR complex constitutes a channel for export of the flagellar proteins involved in axial structure assembly. It also serves as a template for the assembly of the rod structure, which consists ...The FliPQR complex constitutes a channel for export of the flagellar proteins involved in axial structure assembly. It also serves as a template for the assembly of the rod structure, which consists of FliE, FlgB, FlgC, FlgF, and FlgG. FliP, FliQ, and FliR assemble into a right-handed helical structure within the central pore of the flagellar basal body MS-ring, and the complex has two gates on the cytoplasmic and periplasmic sides. The periplasmic gate, formed by the N-terminal α-helices of FliP and FliR, remains closed until six FliE subunits assemble onto FliP and FliR to form the first layer of the rod, but it has remained unclear how each FliE subunit opens the gate and assembles in the absence of the rod cap required for efficient assembly of other rod proteins. Here, we present a cryoelectron microscopy structure of the FliPQR complex in closed form at 3.0 Å resolution. A β-cap, formed by the N-terminal β-strands of FliP and FliR, is located at the top of the FliPQR complex and tightly seals the closed gate. The β-cap has a narrow pore that efficiently and accurately leads the first FliE subunit to its assembly site. Interactions of FliE with FliP and FliR induce a conformational change in FliP and FliR, with their N-terminal α-helices move up and outward to open the gate. Consequently, each of the N-terminal β-strands of FliP and FliR detaches from the β-cap one after another, thereby creating a docking site for the next FliE subunit to efficiently assemble.
History
DepositionOct 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar biosynthetic protein FliP
B: Flagellar biosynthetic protein FliP
C: Flagellar biosynthetic protein FliP
D: Flagellar biosynthetic protein FliP
E: Flagellar biosynthetic protein FliP
F: Flagellar biosynthetic protein FliR
G: Flagellar biosynthetic protein FliQ
H: Flagellar biosynthetic protein FliQ
I: Flagellar biosynthetic protein FliQ
J: Flagellar biosynthetic protein FliQ


Theoretical massNumber of molelcules
Total (without water)202,75310
Polymers202,75310
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Flagellar biosynthetic protein FliP


Mass: 26801.086 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: fliP, flaR, STM1979
Production host: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P54700
#2: Protein Flagellar biosynthetic protein FliR


Mass: 30320.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: fliR, flaP, STM1981
Production host: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P54702
#3: Protein
Flagellar biosynthetic protein FliQ


Mass: 9606.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: fliQ, flaQ, STM1980
Production host: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1L5
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Structure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Source (recombinant)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMtris(hydroxymethyl)aminomethaneTris1
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 III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4885
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1015741
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109333 / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1FLEXIBLE FITREAL
2
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeDetailsSource nameType
17CG4

7cg4

17CG47D84PDBexperimental model
22
32
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413530
ELECTRON MICROSCOPYf_angle_d0.71718451
ELECTRON MICROSCOPYf_dihedral_angle_d12.6764897
ELECTRON MICROSCOPYf_chiral_restr0.0462290
ELECTRON MICROSCOPYf_plane_restr0.0052261

+
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