[English] 日本語
Yorodumi- EMDB-3978: EM map of HasR, a TonB dependent hemophore receptor from Serratia... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3978 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | EM map of HasR, a TonB dependent hemophore receptor from Serratia marcescens. | |||||||||
Map data | HasR is a TonB dependent hemophore receptor from Serratia marcescens. | |||||||||
Sample |
| |||||||||
Biological species | Serratia marcescens (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Prochnicka-Chalufour A / Wojtowicz H / Pehau Arnaudet G / Gubellini F / Fronzes R / Pruneyre-Izadi N | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3978.map.gz | 14.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3978-v30.xml emd-3978.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_3978.png | 31.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3978 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3978 | HTTPS FTP |
-Validation report
Summary document | emd_3978_validation.pdf.gz | 203.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3978_full_validation.pdf.gz | 202.3 KB | Display | |
Data in XML | emd_3978_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3978 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3978 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3978.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | HasR is a TonB dependent hemophore receptor from Serratia marcescens. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : HasR with an amphipol corona covering its membrane embedded part
Entire | Name: HasR with an amphipol corona covering its membrane embedded part |
---|---|
Components |
|
-Supramolecule #1: HasR with an amphipol corona covering its membrane embedded part
Supramolecule | Name: 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 weight | Experimental: 950 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: HasR, a TonB dependent hemophore receptor
Macromolecule | Name: HasR, a TonB dependent hemophore receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Staining | Type: NEGATIVE / Material: Uracyl Acetate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: EMAN2 |
---|---|
Final reconstruction | Applied 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 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |