2020-02-12 REL PDBe PDBe PDBe 2018-06-27 2018-08-22 2019-10-02 2020-02-12 Template-free detection and classification of microsomal membrane bound complexes Martinez-Sanchez A Lucic V Martinez-Sanchez A Kochovski Z Laugks U Meyer Zum Alten Borgloh J Chakraborty S Pfeffer S Baumeister W Lucic V Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms. Nat.Methods US 17 209 216 2020 31907446 doi:10.1038/s41592-019-0675-5 1548-7105 Pfeffer S Burbaum L Unverdorben P Pech M Chen Y Zimmermann R Beckmann R Forster F Structure of the native Sec61 protein-conducting channel. Nat Commun UK 6 8403 2015 26411746 doi:10.1038/ncomms9403 2041-1723 EMD-0074 other EM volume
Same tomograms, different particles
 EMD-0075 other EM volume
Same tomograms, different particles
 EMD-0084 other EM volume
Same tomograms, different particles
 EMD-0085 other EM volume
Same initial particles, different class
 EMD-0086 other EM volume
Same initial particles, different class
 EMD-0087 associated EM volume Canine pancreatic ER vesicles Canine pancreatic ER vesicles 0
The same sample as the one used for EMD-3068 - 72
Canis lupus familiaris pancreas rough endoplasmic reticulum subtomogramAveraging particle 2.0 7.6 20.0 Hepes 50.0 KCl 2.0 MgCl_2
The same as for EMD-3068 - 72
 ETHANE-PROPANE 70 FEI VITROBOT MARK IV
Blot 3 seconds before plunging..
The same sample was used for EMD-3068 - 72
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 3.0 4.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
The same as for EMD-3068 - 72
GATAN K2 SUMMIT (4k x 4k) COUNTING 0.75
The same as for EMD-3068 - 72
 1 C1 16.0 FSC 0.143 CUT-OFF RELION 2200 55 64000 None Template-free, automatic
Biological density was traced based on discrete Morse theory (DisPerSE software) and topological persistence. Particles were picked on the lumenal side of microsomes based on geometric constraints and classified using affinity propagation clustering.
 PyTom 3 4000 RELION MAXIMUM LIKELIHOOD RELION emd_0087.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 419.19998 419.19998 419.19998 90.0 90.0 90.0 X Y Z -0.38757196 0.5854003 0.0022467866 0.032257095 2.62 2.62 2.62 0.0758 AUTHOR Non-translocon associated OST complex AB INITIO MODEL emd_0087_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 419.19998 419.19998 419.19998 90.0 90.0 90.0 X Y Z -0.5105208 0.54461914 0.00090846495 0.0626623 2.62 2.62 2.62 AUTHOR Non-translocon associated OST complex - 1st half emd_0087_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 419.19998 419.19998 419.19998 90.0 90.0 90.0 X Y Z -0.52332944 0.5585199 0.001036335 0.062375646 2.62 2.62 2.62 AUTHOR Non-translocon associated OST complex - 2nd half