REL RCSB RCSB RCSB 2013-06-18 2013-08-21 2013-10-23 2014-02-05 Park E Menetret JF Gumbart JC Ludtke SJ Li W Whynot A Rapoport TA Akey CW ribosome-channel complex, active SecYEG channel, nascent chain, E. coli 70S ribosome Park E Menetret JF Gumbart JC Ludtke SJ Li W Whynot A Rapoport TA Akey CW NATURE 506 102 106 2014 24153188 doi:10.1038/nature12720 3j46 FULLOVERLAP ribosome-nascent chain-SecYEG complex ribosome-nascent chain-SecYEG complex

Sample was prepared by crosslinking the nascent chain within stalled membrane associated ribosomes in bacteria, then purified for cryo-EM.

monomer 5 2.5 membrane-bound 70S ribosome false Escherichia coli EP72 inner membrane 2.5 ribosome-prokaryote: ALL preprotein translocase Escherichia coli EP72 inner membrane 0.0734

SecY: P0AGA2, SecE: P0AG96, SecG: P0AG99

1 heterotrimer true Escherichia coli EP72 pACYC-EhG/Y S1P Escherichia coli 0.061 1 monomer false transfer RNA Escherichia coli 0.025

Both A- and P-site tRNAs present in purified ribosome-nascent chain-SecYEG complex, stalled with SecM sequence

TRANSFER DOUBLE HELIX false singleParticle particle 8 7.2

50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM

400 mesh Quantifoil holey grids with 2/1 or 1.2/1.2

ETHANE 95 77 FEI VITROBOT MARK III

A homemade freezing device with N2 gas driven plunger was also used to prepare grids in a cabinet to maintain humidity.

Blot 1-2 seconds before plunging. FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 160 2.0 1.0 3.0 42000.0 OTHER 94 Carbon grain was imaged at ~175000 times magnification and Thon rings were optimized manually, as visualized on a Fourier transform of ccd images.

Low dose imaging: automated single particle data collection program from TVIPS was used.

2012-02-10 GENERIC TVIPS (4k x 4k) 4900 20

CCD 4k x 4k image frames: best 4900 from ~5900 images used for data processing.

16. Oxford cold holder 0

~450000 particles were selected with e2boxer, used for per ccd frame CTF correction, and then subjected to unsupervised classification to remove aggregates to give 167000 particles. These particles were subjected to supervised classification in 2 steps to give a data set enriched in channels. Particles with the best signal to noise ratio were identified using the FRC comparator from the refinemulti run and classified with e2ligandclassify.py.

per micrograph

OTHER 10.1 OTHER EMAN2

The structure was solved twice: first with a model starting from a 25-Angstrom filtered E. coli ribosome map generated in house, and then a second time using a filtered ribosome model (EMD-5036). In each case, after convergence, maps from two EMAN2 refinements with different parameters were averaged after alignment in Chimera. Four maps in total were averaged to reduce the noise.

53000 5300 2I2P FLEXIBLE FIT Chimera, MDFF REAL 3J01 FLEXIBLE FIT Chimera, MDFF REAL 3I8G B C FLEXIBLE FIT Chimera, MDFF

A- and P-site tRNAs from T. thermophilus ribosome structure. mRNA from this structure also used for some modeling steps.

REAL emd_5693_msk_9.map emd_5693_msk_9.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 100 129 88 -46 -72 -77 129 100 88 211.99998 273.47998 186.56 90.0 90.0 90.0 X Y Z -0.41802311 3.03194666 0.14643894 0.40638983 2.12 2.12 2.12 segmented small subunit

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emd_5693_msk_1.map emd_5693_msk_1.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -98 -93 -100 192 192 192 407.03998 407.03998 407.03998 90.0 90.0 90.0 X Y Z -1.71316838 3.24496651 0.04185728 0.23040985 2.12 2.12 2.12 segmented large ribosomal subunit

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emd_5693_msk_2.map emd_5693_msk_2.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 48 50 64 -39 -19 -42 50 48 64 101.759995 105.99999 135.68 90.0 90.0 90.0 X Y Z -0.33358499 2.73697472 0.04409197 0.21575955 2.12 2.12 2.12 segmented A and P-site tRNAs

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emd_5693_msk_3.map emd_5693_msk_3.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -98 -93 -100 192 192 192 407.03998 407.03998 407.03998 90.0 90.0 90.0 X Y Z -0.26715687 2.49895334 0.00206619 0.04759175 2.12 2.12 2.12 micelle map from channel density

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emd_5693_msk_4.map emd_5693_msk_4.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 42 39 41 -2 -39 30 39 42 41 89.03999 82.67999 86.92 90.0 90.0 90.0 X Y Z -0.09611352 2.56626678 0.14451101 0.39873809 2.12 2.12 2.12 zoned SecYEG channel

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emd_5693_msk_5.map emd_5693_msk_5.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -98 -93 -100 192 192 192 407.03998 407.03998 407.03998 90.0 90.0 90.0 X Y Z -0.41113278 2.56626678 0.00388604 0.0663215 2.12 2.12 2.12 full channel density with micelle and nascent chain

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emd_5693_msk_6.map emd_5693_msk_6.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -98 -93 -100 192 192 192 407.03998 407.03998 407.03998 90.0 90.0 90.0 X Y Z -0.09242741 2.03487086 0.00021667 0.01513404 2.12 2.12 2.12 full nascent chain density, excluding fragments in the tunnel

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emd_5693_msk_7.map emd_5693_msk_7.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -98 -93 -100 192 192 192 407.03998 407.03998 407.03998 90.0 90.0 90.0 X Y Z -0.01844709 1.96272898 0.00011734 0.01135785 2.12 2.12 2.12 nascent chain density with signal sequence helix in the channel

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emd_5693_msk_8.map emd_5693_msk_8.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -98 -93 -100 192 192 192 407.03998 407.03998 407.03998 90.0 90.0 90.0 X Y Z -0.30115208 2.50390124 0.00101317 0.03403844 2.12 2.12 2.12 segmented S1 density, excluding flexible fragments

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