2021-03-03 REL PDBe PDBe PDBe 2020-10-28 2021-02-24 2021-02-24 2021-03-03 Netherlands Organisation for Scientific Research (NWO) 184.034.014 Netherlands In situ subtomogram averaging structure of the type III secretion system of yersinia enterocolitica - basal body Berger C Ravelli RBG Lopez-Iglesias C Kudryashev M Diepold A Peters PJ Berger C Ravelli RBG Lopez-Iglesias C Kudryashev M Diepold A Peters PJ Structure of the Yersinia injectisome in intracellular host cell phagosomes revealed by cryo FIB electron tomography. J.Struct.Biol. US 213 107701 107701 2021 33549695 doi:10.1016/j.jsb.2021.107701 1095-8657 0803 JSBIEM EMD-11905 other EM volume EMD-11906 associated EM volume Basal body of the Type III secretion system of Yersinia enterocolitica Basal body of the Type III secretion system of Yersinia enterocolitica 0 1 Yersinia enterocolitica E40 subtomogramAveraging cell 7.4
CElls were grown in RPMI 1640 medium on the grid. 2 ul of RPMI 1640 was applied to the grid just prior to vitrification
 UltrAuFoil R2/2 GOLD 200 GOLD HOLEY ETHANE 85 310 HOMEMADE PLUNGER
FEI vitrobot modified with a jet-vitrification module and a blotforce feedback mechanism..
FEI TECNAI ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 -0.005 NITROGEN FEI FALCON III (4k x 4k) COUNTING 24.0 2.86 1
Tilt-series aligned and reconstructed with IMOD with gold fiducials.
C3 33.0 FSC 0.143 CUT-OFF Dynamo 1.1.401 141 63 202 averaged from data after manual alignment manually picked Dynamo 1.1.401
4x binned tomograms were filtered with EMDeconvolution for manual picking. Coordinates were transformed to extract particles from 2x binned tomograms after CTF correction and without filtering.
 IMOD 4
CTF correction performed with IMOD
 NOT APPLICABLE Dynamo 1.1.401 emd_11906.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 1395.712 1395.712 1395.712 90.0 90.0 90.0 X Y Z -12.10658 21.579718 -0.1892439 0.6078022 5.452 5.452 5.452 0.32 AUTHOR Subtomogram average structure of the type III secretion system of yersinia enterocolitica - focused on the basal body. emd_11906_msk_1.map emd_11906_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 1395.712 1395.712 1395.712 90.0 90.0 90.0 X Y Z -4.2078805 4.078863 -0.18923305 0.28666693 5.452 5.452 5.452 AUTHOR Subtomogram average structure of the type III secretion system of yersinia enterocolitica - focused on the basal body and filtered to 3.3 nm resolution. emd_11906_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 1395.712 1395.712 1395.712 90.0 90.0 90.0 X Y Z -11.498749 14.064766 -0.15851197 0.67291343 5.452 5.452 5.452 AUTHOR half map of all the odd particles emd_11906_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 1395.712 1395.712 1395.712 90.0 90.0 90.0 X Y Z -10.179272 9.406018 -0.1454808 0.63229376 5.452 5.452 5.452 AUTHOR half map of all the even particles