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- EMDB-46778: E. coli TonB-ExbBD TonB bound to ExbB chain C -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-46778
TitleE. coli TonB-ExbBD TonB bound to ExbB chain C
Map dataTonB-ExbBD with TonB bound to ExbB chainC
Sample
  • Complex: TonB-ExbBD complex
    • Protein or peptide: Biopolymer transport protein ExbB
    • Protein or peptide: Protein TonB
    • Protein or peptide: Biopolymer transport protein ExbD
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsTon system / TRANSPORT PROTEIN
Function / homology
Function and homology information


receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / transmembrane transporter complex / plasma membrane protein complex ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / transmembrane transporter complex / plasma membrane protein complex / protein import / cell envelope / transmembrane transporter activity / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / protein stabilization / protein domain specific binding / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / TonB polyproline region / Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB-system energizer ExbB type-1 / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB system transport protein ExbD type-1 / TonB/TolA, C-terminal ...: / TonB polyproline region / Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB-system energizer ExbB type-1 / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB system transport protein ExbD type-1 / TonB/TolA, C-terminal / : / 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
Protein TonB / Biopolymer transport protein ExbB / Biopolymer transport protein ExbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsCelia H / Botos I
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA DK011011-17 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of the E. coli Ton and Tol motor complexes
Authors: Celia H / Botos I / Ghirlando R / Duche D / Beach BM / Lloubes R / Buchanan SK
History
DepositionAug 28, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46778.png

Downloads & links

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Map

FileDownload / File: emd_46778.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTonB-ExbBD with TonB bound to ExbB chainC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.16394104 - 0.47020903
Average (Standard dev.)-0.00031592866 (±0.017716283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap B

Fileemd_46778_half_map_1.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap A

Fileemd_46778_half_map_2.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TonB-ExbBD complex

EntireName: TonB-ExbBD complex
Components
  • Complex: TonB-ExbBD complex
    • Protein or peptide: Biopolymer transport protein ExbB
    • Protein or peptide: Protein TonB
    • Protein or peptide: Biopolymer transport protein ExbD
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: TonB-ExbBD complex

SupramoleculeName: TonB-ExbBD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: TonB bound to ExbB chainC
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Biopolymer transport protein ExbB

MacromoleculeName: Biopolymer transport protein ExbB / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
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

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Macromolecule #2: Protein TonB

MacromoleculeName: Protein TonB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 28.495709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTLDLPRRFP WPTLLSVCIH GAVVAGLLYT SVHQVIELPA PAQPISVTMV TPADLEPPQA VQPPPEPVVE PEPEPEPIPE PPKEAPVVI EKPKPKPKPK PKPVKKVQEQ PKRDVKPVES RPASPFENTA PARLTSSTAT AATSKPVTSV ASGPRALSRN Q PQYPARAQ ...String:
MTLDLPRRFP WPTLLSVCIH GAVVAGLLYT SVHQVIELPA PAQPISVTMV TPADLEPPQA VQPPPEPVVE PEPEPEPIPE PPKEAPVVI EKPKPKPKPK PKPVKKVQEQ PKRDVKPVES RPASPFENTA PARLTSSTAT AATSKPVTSV ASGPRALSRN Q PQYPARAQ ALRIEGQVKV KFDVTPDGRV DNVQILSAKP ANMFEREVKN AMRRWRYEPG KPGSGIVVNI LFKINGTTEI QG GGSENLY FQGGSAWSHP QFEK

UniProtKB: Protein TonB

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Macromolecule #3: Biopolymer transport protein ExbD

MacromoleculeName: Biopolymer transport protein ExbD / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.161674 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAMHLNENLD DNGEMHDINV TPFIDVMLVL LIIFMVAAPL ATVDVKVNLP ASTSTPQPRP EKPVYLSVKA DNSMFIGNDP VTDETMITA LNALTEGKKD TTIFFRADKT VDYETLMKVM DTLHQAGYLK IGLVGEETAK AKENLYFQGN AGSGHHHHHH H HHH

UniProtKB: Biopolymer transport protein ExbD

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Macromolecule #4: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 4 / Number of copies: 2 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 69.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227584
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ddo:
E. coli TonB-ExbBD TonB bound to ExbB chain C

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