[English] 日本語
Yorodumi
- PDB-9lu9: The chimeric flagellar motor complex between MotA1B1 from Paeniba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lu9
TitleThe chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 1
Components
  • Flagellar motor protein MotA
  • MotB1,Motility protein B
KeywordsMOTOR PROTEIN / Flagellar / motility / Paenibacillus
Function / homology
Function and homology information


bacterial-type flagellum stator complex / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / proton channel activity / bacterial-type flagellum-dependent cell motility / proton transmembrane transport / chemotaxis / protein transport / plasma membrane
Similarity search - Function
Motility protein A, N-terminal / Motility protein A N-terminal / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / : / OmpA-like domain profile. / OmpA-like domain superfamily ...Motility protein A, N-terminal / Motility protein A N-terminal / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain
Similarity search - Domain/homology
Lauryl Maltose Neopentyl Glycol / Flagellar motor protein MotA / Motility protein B
Similarity search - Component
Biological speciesPaenibacillus sp. TCA20 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOnoe, S. / Nishikino, T. / Kinoshita, M. / Kishikawa, J. / Kato, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101XXX. Japan
Japan Society for the Promotion of Science (JSPS)JP23K14157 Japan
Japan Society for the Promotion of Science (JSPS)JP22K18359 Japan
CitationJournal: Biomolecules / Year: 2025
Title: Cryo-EM Structure of the Flagellar Motor Complex from sp. TCA20.
Authors: Sakura Onoe / Tatsuro Nishikino / Miki Kinoshita / Norihiro Takekawa / Tohru Minamino / Katsumi Imada / Keiichi Namba / Jun-Ichi Kishikawa / Takayuki Kato /
Abstract: The bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. ...The bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. The flagellar motor is composed of a rotor and stator complexes, with each stator unit functioning as an ion channel that converts flow from outside of cell membrane into rotational motion. sp. TCA20 was discovered in a hot spring, and a structural analysis was conducted on the stator complex using cryo-electron microscopy to elucidate its function. Two of the three structures (Classes 1 and 3) were found to have structural properties typical for other stator complexes. In contrast, in Class 2 structures, the pentamer ring of the A subunits forms a C-shape, with lauryl maltose neopentyl glycol (LMNG) bound to the periplasmic side of the interface between the A and B subunits. This interface is conserved in all stator complexes, suggesting that hydrophobic ligands and lipids can bind to this interface, a feature that could potentially be utilized in the development of novel antibiotics aimed at regulating cell motility and infection.
History
DepositionFeb 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data 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 motor protein MotA
B: Flagellar motor protein MotA
C: Flagellar motor protein MotA
D: Flagellar motor protein MotA
E: Flagellar motor protein MotA
F: MotB1,Motility protein B
G: MotB1,Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,3718
Polymers213,3667
Non-polymers1,0051
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Flagellar motor protein MotA


Mass: 28568.139 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. TCA20 (bacteria) / Gene: TCA2_3717 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069DFV9
#2: Protein MotB1,Motility protein B / Chemotaxis protein MotB


Mass: 35262.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 6xHis on C terminal is purification tag,6xHis on C terminal is purification tag
Source: (gene. exp.) Paenibacillus sp. TCA20 (bacteria), (gene. exp.) Escherichia coli (E. coli)
Gene: motB, b1889, JW1878 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AF06
#3: Chemical ChemComp-AV0 / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside / 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coliCOMPLEX#1-#20RECOMBINANT
2MotACOMPLEX#11RECOMBINANT
3MotB1-MotBCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Paenibacillus sp. TCA20 (bacteria)1499968
33Paenibacillus sp. TCA20 (bacteria)1499968
43Escherichia coli (E. coli)562
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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: 277 K

-
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 magnification: 59000 X / Calibrated magnification: 56818 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 1705 nm / Calibrated defocus max: 3295 nm / Cs: 0.073 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3129
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Spherical aberration corrector: CEOS Cs corrector
Image scansWidth: 5760 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC3.8particle selection
2SerialEMimage acquisition
4cryoSPARC3.8CTF correction
7Cootmodel fitting
9cryoSPARC3.8initial Euler assignment
10cryoSPARC3.8final Euler assignment
11cryoSPARC3.8classification
12cryoSPARC3.83D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 765007
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96359 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementResolution: 3.3→3.3 Å / Cor.coef. Fo:Fc: 0.728 / SU B: 27.256 / SU ML: 0.398 / ESU R: 0.888
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.39528 --
obs0.39528 63351 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 99.02 Å2
Refinement stepCycle: 1 / Total: 9858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01210018
ELECTRON MICROSCOPYr_bond_other_d00.0169777
ELECTRON MICROSCOPYr_angle_refined_deg1.5931.62813583
ELECTRON MICROSCOPYr_angle_other_deg0.5361.54922682
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.43151274
ELECTRON MICROSCOPYr_dihedral_angle_2_deg19.14549
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.496101767
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.090.21648
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0211104
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021829
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it10.0688.8695117
ELECTRON MICROSCOPYr_mcbond_other10.0678.8695117
ELECTRON MICROSCOPYr_mcangle_it16.59213.296384
ELECTRON MICROSCOPYr_mcangle_other16.59113.2996385
ELECTRON MICROSCOPYr_scbond_it14.00311.3164901
ELECTRON MICROSCOPYr_scbond_other14.00211.3214902
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other23.86316.1877200
ELECTRON MICROSCOPYr_long_range_B_refined34.540312
ELECTRON MICROSCOPYr_long_range_B_other34.540313
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.218 4701 -
obs--100 %

+
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