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- EMDB-4187: EM map of HasR, a TonB dependent receptor from Serratia marcescen... -

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Basic information

Entry
Database: EMDB / ID: EMD-4187
TitleEM map of HasR, a TonB dependent receptor from Serratia marcescens in complex with the hemophore HasA and heme.
Map datathe complex of HasR receptor with heme and HasA protein
Sample
  • Complex: complex of HasR receptor with its hemophore HasA and heme
    • Protein or peptide: HasR in complex with HasA and heme
Biological speciesSerratia marcescens (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsProchnicka-Chalufour A / Wojtowicz H / Pehau-Arnaudet G / Gubellini F / Fronzes R / Izadi-Pruneyre 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 ...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.
History
DepositionNov 30, 2017-
Header (metadata) releaseDec 13, 2017-
Map releaseDec 13, 2017-
UpdateDec 13, 2017-
Current statusDec 13, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4187.png

Downloads & links

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Map

FileDownload / File: emd_4187.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe complex of HasR receptor with heme and HasA protein
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033 / Movie #1: 0.033
Minimum - Maximum-0.06720298 - 0.14553033
Average (Standard dev.)0.00067757926 (±0.010970789)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0670.1460.001

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Supplemental data

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Sample components

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Entire : complex of HasR receptor with its hemophore HasA and heme

EntireName: complex of HasR receptor with its hemophore HasA and heme
Components
  • Complex: complex of HasR receptor with its hemophore HasA and heme
    • Protein or peptide: HasR in complex with HasA and heme

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Supramolecule #1: complex of HasR receptor with its hemophore HasA and heme

SupramoleculeName: complex of HasR receptor with its hemophore HasA and heme
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: An amphipol corona covers the membrane embedded part of the complex
Source (natural)Organism: Serratia marcescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 1.14 MDa

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Macromolecule #1: HasR in complex with HasA and heme

MacromoleculeName: HasR in complex with HasA and heme / type: protein_or_peptide / ID: 1 / Details: HasR: residues 1-865 HasA: residues 866-1071 / Enantiomer: LEVO
SequenceString: AQAEASSAQA AQQKNFNIAA QPLQSAMLRF AEQAGMQVFF DEVKLDGMQA AALNGSMSVE QGLRRLIGGN PVAFRLQPQG QIVLSRLPTA NGDGGALALD SLTVLGAGGN NANDWVYDEP RSVSVISREQ MDNRPARHAA DILEQTTGAY SSVSQQDPAL SVNIRGIQDY ...String:
AQAEASSAQA AQQKNFNIAA QPLQSAMLRF AEQAGMQVFF DEVKLDGMQA AALNGSMSVE QGLRRLIGGN PVAFRLQPQG QIVLSRLPTA NGDGGALALD SLTVLGAGGN NANDWVYDEP RSVSVISREQ MDNRPARHAA DILEQTTGAY SSVSQQDPAL SVNIRGIQDY GRVNMNIDGM RQNFQKSGHG QRNGTMYIDS ELLSGVTIDK GTTGGMGSAG TLGGIATFNT VSASDFLAPG KELGGKLHAS TGDNGTHFIG SGILALGNET GDILLAASER HLGDYWPGNK GDIGNIRINN DTGNYDRYAE SIKNNKIPDT HYRMHSRLAK VGWNLPANQR LQLSYLQTQT ASPIAGTLTN LGTRPPYELG WKRTGYTDVM ARNAAFDYSL APEDVDWLDF QAKLYYVDTQ DDSDTYSTSS LLDNGYATRT RLRTYGAQAQ NTSRFSLAPG HDFRANYGLE FYYDKATSDS SRQGMEGVTA GNRSVASLFA NLTYDYDGWL TLEGGLRYDR YRLRGQTGLS YPDLAKDGQR YTIDNPCKAL RLTGCSTTTR EDWDVDRDQG KLSPTLAVAV RPGVEWLELY TTYGKSWRPP AITETLTNGS AHSSSTQYPN PFLQPERSRA WEVGFNVQQP DLWFEGDRLV AKVAYFDTKV DNYINLAIDR NKPGLVQPSI GNAAYVNNLS KTRFRGLEYQ LNYDAGVFYA DLTYTHMIGK NEFCSNKAWL GGRLRYGDGS RRGNFYVEPD AASNDFVTCD GGTQFGSAAY LPGDRGSVTL GGRAFDRKLD AGVTVRFAPG YQDSSVPSNY PYLADWPKYT LFDLYASYKL TDSLTLRGSV ENLTNRAYVV SYGETLANTL GRGRTVQGGV EYRF MRGSH HHHHHGIRMR ARYPAFSVNY DSSFGGYSIH DYLGQWASTF GDVNHTNGNV TDANSGGFYG GSLSGSQYAI SSTANQVTAF VAGGNLTYTL FNEPAHTLYG QLDSLSFGDG LSGGDTSPYS IQVPDVSFGG LNLSSLQAQG HDGVVHQVVY GLMSGDTGAL ETALNGILDD YGLSVNSTFD QVAAATAVGV QHADSPELLA A

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: EMAN2
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3csl

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 9171
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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