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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: EMD-3978
TitleEM map of HasR, a TonB dependent hemophore receptor from Serratia marcescens.
Map dataHasR is a TonB dependent hemophore receptor from Serratia marcescens.
Sample
  • Organelle or cellular component: HasR with an amphipol corona covering its membrane embedded part
    • Protein or peptide: HasR, a TonB dependent hemophore receptor
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 / 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 ...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 8, 2017-
Header (metadata) releaseNov 22, 2017-
Map releaseNov 22, 2017-
UpdateNov 22, 2017-
Current statusNov 22, 2017Processing site: PDBe / Status: Released

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Structure visualization

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

emd_3978.png

Downloads & links

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Map

FileDownload / File: emd_3978.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHasR is a TonB dependent hemophore receptor from Serratia marcescens.
Voxel sizeX=Y=Z: 1.9 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.06514373 - 0.13357235
Average (Standard dev.)0.00040390805 (±0.0096665295)
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-0.0650.1340.000

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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
Components
  • Organelle or cellular component: HasR with an amphipol corona covering its membrane embedded part
    • Protein or peptide: HasR, a TonB dependent hemophore receptor

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Supramolecule #1: HasR with an amphipol corona covering its membrane embedded part

SupramoleculeName: HasR with an amphipol corona covering its membrane embedded part
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Serratia marcescens (bacteria)
Molecular weightExperimental: 950 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: HasR, a TonB dependent hemophore receptor

MacromoleculeName: HasR, a TonB dependent hemophore receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: AQAEASSAQA AQQKNFNIAA QPLQSAMLRF AEQAGMQVFF DEVKLDGMQA AALNGSMSVE GLRRLIGGNP VAFRLQPQGQ IVLSRLPTAN GDGGALALDS LTVLGAGGNN ANDWVYDEPR SVSVISREQM DNRPARHAAD ILEQTTGAYS SVSQQDPAL SVNIRGIQDY ...String:
AQAEASSAQA AQQKNFNIAA QPLQSAMLRF AEQAGMQVFF DEVKLDGMQA AALNGSMSVE GLRRLIGGNP VAFRLQPQGQ IVLSRLPTAN GDGGALALDS LTVLGAGGNN ANDWVYDEPR SVSVISREQM DNRPARHAAD ILEQTTGAYS SVSQQDPAL SVNIRGIQDY GRVNMNIDGM RQNFQKSGHG QRNGTMYIDS ELLSGVTIDK GTTGGMGSAG TLGGIATFNT VSASDFLAPG KELGGKLHA STGDNGTHFI GSGILALGNE TGDILLAASE RHLGDYWPGN KGDIGNIRIN NDTGNYDRYA ESIKNNKIPD T HYRMHSRL AKVGWNLPAN QRLQLSYLQT QTASPIAGTL TNLGTRPPYE LGWKRTGYTD VMARNAAFDY SLAPEDVDWL DF QAKLYYV DTQDDSDTYS TSSLLDNGYA TRTRLRTYGA QAQNTSRFSL APGHDFRANY GLEFYYDKAT SDSSRQGMEG VTP AGNRSV ASLFANLTYD YDGWLTLEGG LRYDRYRLRG QTGLSYPDLA KDGQRYTIDN PCKALRLTGC STTTREDWDV DRDQ GKLSP TLAVAVRPGV EWLELYTTYG KSWRPPAITE TLTNGSAHSS STQYPNPFLQ PERSRAWEVG FNVQQPDLWF EGDRL VAKV AYFDTKVDNY INLAIDRNKP GLVQPSIGNA AYVNNLSKTR FRGLEYQLNY DAGVFYADLT YTHMIGKNEF CSNKAW LGG RLRYGDGSRR GNFYVEPDAA SNDFVTCDGG TQFGSAAYLP GDRGSVTLGG RAFDRKLDAG VTVRFAPGYQ DSSVPSNYPY LADWPKYTLF DLYASYKLTD SLTLRGSVEN LTNRAYVVSY GETLANTLGR GRTVQGGVEY RF

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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: Uracyl Acetate

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Electron microscopy

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

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Image processing

CTF correctionSoftware - Name: EMAN2
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
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: 14158

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