[English] 日本語
Yorodumi
- EMDB-63392: The chimeric flagellar motor complex between MotA1B1 from Paeniba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63392
TitleThe chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 1
Map data
Sample
  • Complex: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
    • Complex: MotA
      • Protein or peptide: Flagellar motor protein MotA
    • Complex: MotB1-MotB
      • Protein or peptide: MotB1,Motility protein B
  • Ligand: Lauryl Maltose Neopentyl Glycol
KeywordsFlagellar / motility / Paenibacillus / MOTOR PROTEIN
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
Flagellar motor protein MotA / Motility protein B
Similarity search - Component
Biological speciesPaenibacillus sp. TCA20 (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOnoe S / Nishikino T / Kinoshita M / Kishikawa J / Kato T
Funding support Japan, 3 items
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, 2025-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63392.png

Downloads & links

-
Map

FileDownload / File: emd_63392.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.6621827 - 1.0245645
Average (Standard dev.)0.00076670264 (±0.035842475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 225.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_63392_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63392_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The chimeric flagellar motor complex between MotA1B1 from Paeniba...

EntireName: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
Components
  • Complex: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
    • Complex: MotA
      • Protein or peptide: Flagellar motor protein MotA
    • Complex: MotB1-MotB
      • Protein or peptide: MotB1,Motility protein B
  • Ligand: Lauryl Maltose Neopentyl Glycol

-
Supramolecule #1: The chimeric flagellar motor complex between MotA1B1 from Paeniba...

SupramoleculeName: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 150 KDa

-
Supramolecule #2: MotA

SupramoleculeName: MotA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Paenibacillus sp. TCA20 (bacteria)

-
Supramolecule #3: MotB1-MotB

SupramoleculeName: MotB1-MotB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Paenibacillus sp. TCA20 (bacteria)

-
Macromolecule #1: Flagellar motor protein MotA

MacromoleculeName: Flagellar motor protein MotA / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. TCA20 (bacteria)
Molecular weightTheoretical: 28.568139 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDIATLIGLI AGAVAIIGGF LWEGGQITGL FQGTAALIVF GGTIAAVLIS YPMHRIRTLP AGIKLAFKPN RSEVNEWLED IVEMSMVAR REGVLALEQK VLDHPNIFLR EGIQLVVDGT DQPIVRQIME LDIDAKEQEH DNYAKLFESA GSYAPTMGII G TVMGLIQV ...String:
MDIATLIGLI AGAVAIIGGF LWEGGQITGL FQGTAALIVF GGTIAAVLIS YPMHRIRTLP AGIKLAFKPN RSEVNEWLED IVEMSMVAR REGVLALEQK VLDHPNIFLR EGIQLVVDGT DQPIVRQIME LDIDAKEQEH DNYAKLFESA GSYAPTMGII G TVMGLIQV LGHLTDPSQL GPSIAVAFIA TLYGVASANL IFLPIASKIR AKSAEEILVM EMILEGVLSV QNGDNALLVR KK LNTYITS QPTSLNPRKD VTHETAE

UniProtKB: Flagellar motor protein MotA

-
Macromolecule #2: MotB1,Motility protein B

MacromoleculeName: MotB1,Motility protein B / type: protein_or_peptide / ID: 2
Details: 6xHis on C terminal is purification tag,6xHis on C terminal is purification tag
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.262496 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRQRNRRTRN VKSAHSSGSP HDRWMITYAD LITLLLIFFV MMYAMSRLDA SKYEEVTSSL QTTFQSSSGI LDGGNGVIDY PSGQNGNSS SEANQPGSSG TGSDMGQEAD GGPLTERESR LRKLRGDLDQ LIESDPKLRA LRPHLKIDLV QEGLRIQIID S QNRPMFRT ...String:
MRQRNRRTRN VKSAHSSGSP HDRWMITYAD LITLLLIFFV MMYAMSRLDA SKYEEVTSSL QTTFQSSSGI LDGGNGVIDY PSGQNGNSS SEANQPGSSG TGSDMGQEAD GGPLTERESR LRKLRGDLDQ LIESDPKLRA LRPHLKIDLV QEGLRIQIID S QNRPMFRT GSADVEPYMR DILRAIAPVL NGIPNRISLS GHTDDFPYAS GEKGYSNWEL SADRANASRR ELMVGGLDSG KV LRVVGMA ATMRLSDRGP DDAVNRRISL LVLNKQAEQA ILHENAESQN EPVSALEKPE VAPQVSVPTM PSAEPRHHHH HH

UniProtKB: Motility protein B

-
Macromolecule #3: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 3 / Number of copies: 1 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: CEOS Cs corrector / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3129 / Average exposure time: 3.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.295 µm / Calibrated defocus min: 1.705 µm / Calibrated magnification: 56818 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.073 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 765007
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.8) / Number images used: 96359
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.8)
Final 3D classificationNumber classes: 6 / Avg.num./class: 40000 / Software - Name: cryoSPARC (ver. 3.8)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9lu9:
The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 1

+
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