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- EMDB-3978: EM map of HasR, a TonB dependent hemophore receptor from Serratia... -

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Basic information

Entry
Database: EMDB / ID: 3978
TitleEM map of HasR, a TonB dependent hemophore receptor from Serratia marcescens.
Map dataHasR is a TonB dependent hemophore receptor from Serratia marcescens.
SampleHasR with an amphipol corona covering its membrane embedded part
  • HasR, a TonB dependent hemophore receptor
SourceSerratia marcescens (bacteria)
Methodsingle particle reconstruction / 23 Å resolution
AuthorsProchnicka-Chalufour A / Wojtowicz H / Pehau Arnaudet G / Gubellini F / Fronzes R / Pruneyre-Izadi N
CitationJournal: Biochem. J. / Year: 2016
Title: Structural basis of the signalling through a bacterial membrane receptor HasR deciphered by an integrative approach.
Authors: Halina Wojtowicz / Ada Prochnicka-Chalufour / Gisele Cardoso de Amorim / Olga Roudenko / Catherine Simenel / Idir Malki / Gérard Pehau-Arnaudet / Francesca Gubellini / Alexandros Koutsioubas / Javier Pérez / Philippe Delepelaire / Muriel Delepierre / Rémi Fronzes / Nadia Izadi-Pruneyre
Abstract: Bacteria use diverse signalling pathways to adapt gene expression to external stimuli. In Gram-negative bacteria, the binding of scarce nutrients to membrane transporters triggers a signalling ...Bacteria use diverse signalling pathways to adapt gene expression to external stimuli. In Gram-negative bacteria, the binding of scarce nutrients to membrane transporters triggers a signalling process that up-regulates the expression of genes of various functions, from uptake of nutrient to production of virulence factors. Although proteins involved in this process have been identified, signal transduction through this family of transporters is not well understood. In the present study, using an integrative approach (EM, SAXS, X-ray crystallography and NMR), we have studied the structure of the haem transporter HasR captured in two stages of the signalling process, i.e. before and after the arrival of signalling activators (haem and its carrier protein). We show for the first time that the HasR domain responsible for signal transfer: (i) is highly flexible in two stages of signalling; (ii) extends into the periplasm at approximately 70-90 Å (1 Å=0.1 nm) from the HasR β-barrel; and (iii) exhibits local conformational changes in response to the arrival of signalling activators. These features would favour the signal transfer from HasR to its cytoplasmic membrane partners.
DateDeposition: Nov 8, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3978.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.9 Å/pix.
= 304. Å
160 pix
1.9 Å/pix.
= 304. Å
160 pix
1.9 Å/pix.
= 304. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.9 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.06514373 - 0.13357235
Average (Standard dev.)0.00040390805 (0.0096665295)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
CellA=B=C: 304 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.91.91.9
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z304.000304.000304.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0650.1340.000

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Supplemental data

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Sample components

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Entire HasR with an amphipol corona covering its membrane embedded part

EntireName: HasR with an amphipol corona covering its membrane embedded part
Number of components: 2
MassExperimental: 950 kDa

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Component #1: cellular-component, HasR with an amphipol corona covering its mem...

Cellular-componentName: HasR with an amphipol corona covering its membrane embedded part
Recombinant expression: No
MassExperimental: 950 kDa
SourceSpecies: Serratia marcescens (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, HasR, a TonB dependent hemophore receptor

ProteinName: HasR, a TonB dependent hemophore receptor / Recombinant expression: No

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 7.5
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 14158
3D reconstructionSoftware: RELION / Resolution: 23 Å / Resolution method: FSC 0.143 CUT-OFF

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