[English] 日本語
Yorodumi
- EMDB-6927: Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6927
TitleStructure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
Map data
Sample
  • Complex: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
    • Protein or peptide: Biopolymer transport protein ExbB
    • Protein or peptide: 22-mer peptide from Biopolymer transport protein ExbD
KeywordsTon system / ion channel / energizer / transporter / proton motive force / TRANSPORT PROTEIN
Function / homology
Function and homology information


ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter complex / transmembrane transporter activity / cell outer membrane ...ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter complex / transmembrane transporter activity / cell outer membrane / protein transport / intracellular iron ion homeostasis / protein stabilization / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
TonB-system energizer ExbB type-1 / TonB system transport protein ExbD type-1 / : / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Biopolymer transport protein ExbB / Biopolymer transport protein ExbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsYonekura K / Yamashita Y / Matsuoka R / Maki-Yonekura S
Funding support Japan, 2 items
OrganizationGrant numberCountry
the Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research15K06986 Japan
the Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research16H04757 Japan
CitationJournal: Elife / Year: 2018
Title: Hexameric and pentameric complexes of the ExbBD energizer in the Ton system.
Authors: Saori Maki-Yonekura / Rei Matsuoka / Yoshiki Yamashita / Hirofumi Shimizu / Maiko Tanaka / Fumie Iwabuki / Koji Yonekura /
Abstract: Gram-negative bacteria import essential nutrients such as iron and vitamin B through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three ...Gram-negative bacteria import essential nutrients such as iron and vitamin B through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three inner membrane proteins, ExbB, ExbD and TonB. ExbB and ExbD form the proton channel that energizes uptake through TonB. Recently, crystal structures suggest that the ExbB pentamer is the scaffold. Here, we present structures of hexameric complexes of ExbB and ExbD revealed by X-ray crystallography and single particle cryo-EM. Image analysis shows that hexameric and pentameric complexes coexist, with the proportion of hexamer increasing with pH. Channel current measurement and 2D crystallography support the existence and transition of the two oligomeric states in membranes. The hexameric complex consists of six ExbB subunits and three ExbD transmembrane helices enclosed within the central channel. We propose models for activation/inactivation associated with hexamer and pentamer formation and utilization of proton motive force.
History
DepositionMar 7, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseMay 9, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.039
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.039
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5zfu
  • Surface level: 0.039
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6927.png

Downloads & links

-
Map

FileDownload / File: emd_6927.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.)
1.22 Å/pix.
x 256 pix.
= 311.219 Å		1.22 Å/pix.
x 256 pix.
= 311.219 Å		1.22 Å/pix.
x 256 pix.
= 311.219 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2157 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.039 / Movie #1: 0.039
Minimum - Maximum-0.056289624 - 0.14762536
Average (Standard dev.)0.00025495357 (±0.0046866513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 311.2192 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.215699218751.215699218751.21569921875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z311.219311.219311.219
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0560.1480.000

-
Supplemental data

-
Sample components

-
Entire : the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)

EntireName: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
Components
  • Complex: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
    • Protein or peptide: Biopolymer transport protein ExbB
    • Protein or peptide: 22-mer peptide from Biopolymer transport protein ExbD

-
Supramolecule #1: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)

SupramoleculeName: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12

-
Macromolecule #1: Biopolymer transport protein ExbB

MacromoleculeName: Biopolymer transport protein ExbB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 26.312322 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGNNLMQTDL SVWGMYQHAD IVVKCVMIGL ILASVVTWAI FFSKSVEFFN QKRRLKREQQ LLAEARSLNQ ANDIAADFGS KSLSLHLLN EAQNELELSE GSDDNEGIKE RTSFRLERRV AAVGRQMGRG NGYLATIGAI SPFVGLFGTV WGIMNSFIGI A QTQTTNLA ...String:
MGNNLMQTDL SVWGMYQHAD IVVKCVMIGL ILASVVTWAI FFSKSVEFFN QKRRLKREQQ LLAEARSLNQ ANDIAADFGS KSLSLHLLN EAQNELELSE GSDDNEGIKE RTSFRLERRV AAVGRQMGRG NGYLATIGAI SPFVGLFGTV WGIMNSFIGI A QTQTTNLA VVAPGIAEAL LATAIGLVAA IPAVVIYNVF ARQIGGFKAM LGDVAAQVLL LQSRDLDLEA SAAAHPVRVA QK LRAG

UniProtKB: Biopolymer transport protein ExbB

-
Macromolecule #2: 22-mer peptide from Biopolymer transport protein ExbD

MacromoleculeName: 22-mer peptide from Biopolymer transport protein ExbD / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 2.430062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NVTPFIDVML VLLIIFMVAA PL

UniProtKB: Biopolymer transport protein ExbD

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.81195 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38323
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5zfu:
Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)

+
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