REL PDBe PDBe PDBe 2015-07-01 2015-07-15 2015-09-30 2016-02-17 Mammalian ribosome bound to the native Sec61 protein-conducting channel in the 'non-inserting' state ('conventional' alignment) Pfeffer S Burbaum L Unverdorben P Pech M Chen Y Zimmermann R Beckmann R Foerster F Ribosome, Sec61, Translocon, Endoplasmic Reticulum, Cryoelectron Tomography, Subtomogram Analysis Pfeffer S Burbaum L Unverdorben P Pech M Chen Y Zimmermann R Beckmann R Foerster F Structure of the native Sec61 protein-conducting channel. NAT.COMMUN. 6 8403 8403 2015 26411746 doi:10.1038/ncomms9403 5a6u FULLOVERLAP Mammalian ribosome bound to the native protein translocon on canine pancreatic ER vesicles Mammalian ribosome bound to the native protein translocon on canine pancreatic ER vesicles 2 Membrane-bound 80S ribosome false Canis lupus familiaris Dog Pancreas ribosome-eukaryote: ALL ER protein translocon Canis lupus familiaris Dog Pancreas Endoplasmic Reticulum false subtomogramAveraging particle 2 7.6
20mM Hepes, 50mM KCl; 2mM MgCl2
Lacey carbon molybdenum grid
 ETHANE-PROPANE MIXTURE 70 FEI VITROBOT MARK IV Blot 3 seconds before plunging. FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 3.0 4.0 FEI TITAN KRIOS AUTOGRID HOLDER Gatan 2014-06-18 GATAN K2 (4k x 4k) 30 -20 20
Tomogram reconstruction and template matching against a single particle cryo-EM reconstruction of the 80S ribosome were accomplished using PyTom. Subtomograms extracted from cross correlation peaks in the tomogram were classified using constrained principal component analysis focusing on the large ribosomal subunit and the ER membrane. For the retained coordinates, 1 x binned subtomograms were reconstructed individually from the weighted back-projections using the full tilt range, iteratively aligned and classified focusing on the translocon. For the retained coordinates, unbinned subtomograms were reconstructed individually from the weighted back-projections using only a reduced tilt range (-20 deg to +20 deg) and iteratively aligned using a 'conventional' subtomogram alignment procedure.
C1 9.0 OTHER PyTom, tom_toolbox, av3_toolbox 17600
Each tilt image
 emd_3068.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 576.39996 576.39996 576.39996 90.0 90.0 90.0 X Y Z -16.746192929999999 20.314157489999999 0.0 0.99999994 2.62 2.62 2.62 3.0 AUTHOR Subtomogram average of non-solubilized ribosome-Sec61 complexes in the 'non-inserting' state. Subtomogram alignment was carried out using 'conventional' alignment.
::::EMDATABANK.org::::EMD-3068::::
 3J7Q 1 2 3 FLEXIBLE FIT MDFF
The Sec61a N-terminal domain along with Sec61b was first fitted as a rigid body prior to flexible fitting.
pseudo-energy REAL