2024-07-10 REL PDBe PDBe PDBe 2020-03-24 2021-03-31 2021-03-31 2024-07-10 French National Research Agency ANR-11-LABEX-0011-01 France Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy Biou V Delepelaire P membrane protein, iron uptake, proton transfer, TonB complex, METAL TRANSPORT Biou V Adaixo RJD Chami M Coureux PD Laurent B Enguene VYN de Amorim GC Izadi-Pruneyre N Malosse C Chamot-Rooke J Stahlberg H Delepelaire P Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog. Commun Biol UK 5 355 355 2022 35418619 doi:10.1038/s42003-022-03306-y 2399-3642 Biou V Chami M Coureux PD Laurent B Ntsogo Y Izadi-Pruneyre N Malosse C Chamot-Rooke J Stahlberg H Delepelaire P Functional and structural characterization of Serratia marcescens ExbB: determinants of the interaction with HasB/TonB Biorxiv US 2021 doi:10.1101/2021.04.21.440815 2692-8205 Scheres SH RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. US 180 519 530 2012 23000701 doi:10.1016/j.jsb.2012.09.006 1095-8657 0803 JSBIEM 6ye4 FULLOVERLAP Homopentamer of ExbB Homopentamer of ExbB 0 1
the expressed sequence corresponds to the mature sequence after signal peptide cleavage.
Serratia marcescens Db11 0.174 Biopolymer transport protein ExbB Serratia marcescens 0.030413621
a 6-histidine tag is present at the C-terminus
5 Escherichia coli BL21(DE3) LEVO APAANPAVTESVAPTTAPAPAAAAPESITPVNPAPTIQPPETRGMDLSIWGMYQHADAVVKAVMIGLVLASIVTWTILFA KGSELLRAKRRLRREQLALAEARSLDEASELAQNFSPESVSAVLLNDAQNELELSAESNDNNGIKERTGFRLERRVAAYS RNMGRGNGFLATIGAISPFVGLFGTVWGIMNSFIGIAHSQTTNLAVVAPGIAEALLATAMGLVAAIPAVVIYNIFARVIS GHRAQVGDVAAQVLLLQGRDLDLAATAEAKRSQHAHQLRAGHHHHHH A0A1C3HJ46 (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE 0.000751023 5 PGT singleParticle particle 0.1 8.0 20.0 tris-HCl 100.0 NaCl Sodium chloride 0.0015 LMNG lauryl maltose neopentyl glycol
20mM Tris-HCl pH 8,0 100mM NaCl 0,0015% LMNG
 Quantifoil R2/4 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 95 277 LEICA EM CPC
the sample was monodisperse as evidenced by gel filtration column
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.5 2.5 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 83.0 93.0 GIF Quantum LS 20 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3710 3838 1-56 1 3122 7.0 55.95
frames were weighted according to electron dose and particle movement during Relion bayesian polishing procedure.
 1
images were processed with Motioncor2
1291382
used ab initio model on a subset of particles
 1 C5 FOURIER SPACE 3.2 FSC 0.143 CUT-OFF RELION 3.0 157111 ANGULAR RECONSTITUTION RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 4 RELION 3.0 emd_10789.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 364 364 364 0 0 0 364 364 364 301.028 301.028 301.028 90.0 90.0 90.0 X Y Z -0.07147077 0.11590917 0.00010691346 0.0022554384 0.827 0.827 0.827 0.012 AUTHOR 5SV0 A 10-234 PDB experimental model FLEXIBLE FIT
the ExbB sequence from S. marcescens was modeled by homology from the 5SV0 monomer from E. coli using Phyre software and the pentamer was generated using the 5SV0 symmetry. real space refinement was carried out with rigid body, simulated annealing and morphing steps.
Correlation coefficient REAL 55.299999999999997 emd_10789_msk_1.map emd_10789_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 364 364 364 0 0 0 364 364 364 301.028 301.028 301.028 90.0 90.0 90.0 X Y Z -0.00904125 0.033014197 0.00010394036 0.0010591701 0.827 0.827 0.827 AUTHOR emd_10789_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 364 364 364 0 0 0 364 364 364 301.028 301.028 301.028 90.0 90.0 90.0 X Y Z -0.019219559 0.042578876 0.000010839935 0.001572886 0.827 0.827 0.827 AUTHOR emd_10789_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 364 364 364 0 0 0 364 364 364 301.028 301.028 301.028 90.0 90.0 90.0 X Y Z -0.020206966 0.04409066 0.000010947237 0.0015754008 0.827 0.827 0.827 AUTHOR