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- EMDB-11806: cryo-EM structure of ExbBD from Serratia Marcescens -

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Basic information

Entry
Database: EMDB / ID: EMD-11806
Titlecryo-EM structure of ExbBD from Serratia Marcescens
Map dataCryosparc sharpened map
Sample
  • Complex: 5-ExbB + 2-ExbD complex
    • Protein or peptide: Biopolymer transport protein ExbB
    • Protein or peptide: Biopolymer transport protein ExbD
KeywordsTonB transport / MEMBRANE PROTEIN / IRON UPTAKE / PROTON TRANSFER / TONB COMPLEX / METAL TRANSPORT / MOTOR PROTEIN
Function / homology
Function and homology information


transmembrane transporter activity / membrane => GO:0016020 / protein transport / 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 speciesSerratia marcescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsBiou V / Adaixo R
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)11-LABX-0011 France
Citation
Journal: Commun Biol / Year: 2022
Title: Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog.
Authors: Valérie Biou / Ricardo Jorge Diogo Adaixo / Mohamed Chami / Pierre-Damien Coureux / Benoist Laurent / Véronique Yvette Ntsogo Enguéné / Gisele Cardoso de Amorim / Nadia Izadi-Pruneyre / ...Authors: Valérie Biou / Ricardo Jorge Diogo Adaixo / Mohamed Chami / Pierre-Damien Coureux / Benoist Laurent / Véronique Yvette Ntsogo Enguéné / Gisele Cardoso de Amorim / Nadia Izadi-Pruneyre / Christian Malosse / Julia Chamot-Rooke / Henning Stahlberg / Philippe Delepelaire /
Abstract: ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The ...ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The opportunistic pathogen Serratia marcescens (Sm) possesses both TonB and a heme-specific TonB paralog, HasB. ExbB has a long periplasmic extension absent in other bacteria such as E. coli (Ec). Long ExbB's are found in several genera of Alphaproteobacteria, most often in correlation with a hasB gene. We investigated specificity determinants of ExbB and HasB. We determined the cryo-EM structures of ExbB and of the ExbB-ExbD complex from S. marcescens. ExbB alone is a stable pentamer, and its complex includes two ExbD monomers. We showed that ExbB extension interacts with HasB and is involved in heme acquisition and we identified key residues in the membrane domain of ExbB and ExbB, essential for function and likely involved in the interaction with TonB/HasB. Our results shed light on the class of inner membrane energy machinery formed by ExbB, ExbD and HasB.
#1: Journal: Biorxiv / Year: 2021
Title: Functional and structural characterization of Serratia marcescens ExbB: determinants of the interaction with HasB/TonB
Authors: Biou V / Chami M / Coureux PD / Laurent B / Ntsogo Y / Izadi-Pruneyre N / Malosse C / Chamot-Rooke J / Stahlberg H / Delepelaire P
History
DepositionSep 29, 2020-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ajq
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11806.png

Downloads & links

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Map

FileDownload / File: emd_11806.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35 / Movie #1: 0.45
Minimum - Maximum-3.1956706 - 2.8116155
Average (Standard dev.)0.00074117066 (±0.07372013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.152 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.152273.152273.152
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-3.1962.8120.001

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Supplemental data

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Half map: half map B

Fileemd_11806_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_11806_half_map_2.map
Annotationhalf map 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 : 5-ExbB + 2-ExbD complex

EntireName: 5-ExbB + 2-ExbD complex
Components
  • Complex: 5-ExbB + 2-ExbD complex
    • Protein or peptide: Biopolymer transport protein ExbB
    • Protein or peptide: Biopolymer transport protein ExbD

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Supramolecule #1: 5-ExbB + 2-ExbD complex

SupramoleculeName: 5-ExbB + 2-ExbD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Serratia marcescens (bacteria)
Molecular weightTheoretical: 150 KDa

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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: Serratia marcescens (bacteria)
Molecular weightTheoretical: 29.584752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: APAANPAVTE SVAPTTAPAP AAAAPESITP VNPAPTIQPP ETRGMDLSIW GMYQHADAVV KAVMIGLVLA SIVTWTILFA KGSELLRAK RRLRREQLAL AEARSLDEAS ELAQNFSPES VSAVLLNDAQ NELELSAESN DNNGIKERTG FRLERRVAAY S RNMGRGNG ...String:
APAANPAVTE SVAPTTAPAP AAAAPESITP VNPAPTIQPP ETRGMDLSIW GMYQHADAVV KAVMIGLVLA SIVTWTILFA KGSELLRAK RRLRREQLAL AEARSLDEAS ELAQNFSPES VSAVLLNDAQ NELELSAESN DNNGIKERTG FRLERRVAAY S RNMGRGNG FLATIGAISP FVGLFGTVWG IMNSFIGIAH SQTTNLAVVA PGIAEALLAT AMGLVAAIPA VVIYNIFARV IS GHRAQVG DVAAQVLLLQ GRDLDLAATA EAKRSQHAHQ LRAG

UniProtKB: Biopolymer transport protein ExbB

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Macromolecule #2: Biopolymer transport protein ExbD

MacromoleculeName: Biopolymer transport protein ExbD / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Serratia marcescens (bacteria)
Molecular weightTheoretical: 16.26869 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAMRLNEDLD DSGELHEINV TPFIDVMLVL LIIFMVAAPL ATVDIRVDLP ASSAKPQPRP EKPVFLSVKA DKQLYVGDQP VNADQLTSV LDQRTQANKE TTIFFQADKS VDYETLMSVM DTLRKAGYLK VGLVGMEGAA KHHHHHH

UniProtKB: Biopolymer transport protein ExbD

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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

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMTris-HCltris
0.0015 %LMNGLauryl Maltose Neopentyl Glycol
GridModel: C-flat / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK II
Detailsthe sample was monodisperse as seen on gel filtration chromatogram

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K / Max: 100.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 4000 / Average exposure time: 12.0 sec. / Average electron dose: 4.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 139000
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

Particle selectionNumber selected: 1373000 / Details: picking on 3028 images with best resolution
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ye4

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.0) / Number images used: 158000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.0)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ye4


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 169 / Target criteria: correlation coefficient
Output model

PDB-7ajq:
cryo-EM structure of ExbBD from Serratia Marcescens

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