[English] 日本語
Yorodumi
- PDB-38lp: Salmonella Flagellar Export Apparatus (FliPQR/FlhB/FlhA) in the c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 38lp
TitleSalmonella Flagellar Export Apparatus (FliPQR/FlhB/FlhA) in the context of the intact basal body with an asymmetric FlhA ring
Components
  • Flagellar biosynthesis protein FlhA
  • Flagellar biosynthetic protein FlhB
  • Flagellar biosynthetic protein FliP
  • Flagellar biosynthetic protein FliQ
  • Flagellar biosynthetic protein FliR
KeywordsPROTEIN TRANSPORT / Flagella / Secretion / PMF
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / protein secretion / bacterial-type flagellum assembly / protein targeting / plasma membrane
Similarity search - Function
Flagellar biosynthetic protein FlhB / Flagellar biosynthesis protein FlhA / FHIPEP, domain 1 / Type III secretion system substrate exporter / FHIPEP conserved site / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 ...Flagellar biosynthetic protein FlhB / Flagellar biosynthesis protein FlhA / FHIPEP, domain 1 / Type III secretion system substrate exporter / FHIPEP conserved site / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Bacterial export protein family 3 / Bacterial export proteins, family 3 / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2.
Similarity search - Domain/homology
Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FlhB / Flagellar biosynthesis protein FlhA / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsJohnson, S. / Johnson, M.K. / Lea, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Structure of the proton-powered secretion motor at the heart of the bacterial flagellum
Authors: Johnson, M.K. / Johnson, S. / Deme, J.C. / Alfaro-Alvarado, L. / Bryant, O.J. / Chevance, F.F.V. / Hughes, K.T. / Lea, S.M.
History
DepositionSep 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A1: Flagellar biosynthetic protein FliP
B1: Flagellar biosynthetic protein FliP
C1: Flagellar biosynthetic protein FliP
D1: Flagellar biosynthetic protein FliP
E1: Flagellar biosynthetic protein FliP
F1: Flagellar biosynthetic protein FliR
G1: Flagellar biosynthetic protein FliQ
H1: Flagellar biosynthetic protein FliQ
I1: Flagellar biosynthetic protein FliQ
J1: Flagellar biosynthetic protein FliQ
K1: Flagellar biosynthetic protein FlhB
A2: Flagellar biosynthesis protein FlhA
B2: Flagellar biosynthesis protein FlhA
C2: Flagellar biosynthesis protein FlhA
D2: Flagellar biosynthesis protein FlhA
E2: Flagellar biosynthesis protein FlhA
F2: Flagellar biosynthesis protein FlhA
G2: Flagellar biosynthesis protein FlhA
H2: Flagellar biosynthesis protein FlhA
I2: Flagellar biosynthesis protein FlhA


Theoretical massNumber of molelcules
Total (without water)918,00120
Polymers918,00120
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 natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P54700
#2: 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 (bacteria)
References: UniProt: P54702
#3: 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 (bacteria)
References: UniProt: P0A1L5
#4: Protein Flagellar biosynthetic protein FlhB


Mass: 42407.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P40727
#5: Protein
Flagellar biosynthesis protein FlhA


Mass: 74913.484 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P40729
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Salmonella Flagellar Export Apparatus (FliPQR/FlhB/FlhA)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 58.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1SIMPLE3particle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51079 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 215.66 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002636085
ELECTRON MICROSCOPYf_angle_d0.651649061
ELECTRON MICROSCOPYf_chiral_restr0.03896130
ELECTRON MICROSCOPYf_plane_restr0.0056041
ELECTRON MICROSCOPYf_dihedral_angle_d5.20574886

+
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