In situ subtomogram average of Rubisco within the Chlamydomonas pyrenoid

2017-10-04 REL PDBe PDBe PDBe 2017-04-26 2017-05-03 2017-05-03 2017-10-04 In situ subtomogram average of Rubisco within the Chlamydomonas pyrenoid Cuellar LK Schaffer M Strauss M Martinez-Sanchez A Plitzko JM Foerster F Engel BD Freeman Rosenzweig ES Xu B Kuhn Cuellar L Martinez-Sanchez A Schaffer M Strauss M Cartwright HN Ronceray P Plitzko JM Forster F Wingreen NS Engel BD Mackinder LCM Jonikas MC The Eukaryotic CO2-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization. Cell 171 148 162.e19 2017 28938114 doi:10.1016/j.cell.2017.08.008 1097-4172 EMD-3694 associated EM volume In situ Rubisco holoenzyme In situ Rubisco holoenzyme 0 1

In situ subtomogram average generated from Rubisco holoenzymes imaged within the native Chlamydomonas pyrenoid. Cells were thinned by focused ion beam milling.

Chlamydomonas reinhardtii mat3-4 0.54 Rubisco holoenzyme LEVO MVPQTETKAGAGFKAGVKDYRLTYYTPDYVVRDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVPGEDNQYIAYVAYPIDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGPPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVCAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLAKALRMSGGDHLHSGTVVGKLEGEREVTLGFVDLMRDDYVEKDRSRGIYFTQDWCSMPGVMPVASGGIHVWHMPALVEIFGDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQARNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL 4.1.1.39 subtomogramAveraging cell 7. Quantifoil R2/1 COPPER 200 GLOW DISCHARGE AIR ETHANE-PROPANE 90 293 FEI VITROBOT MARK IV

Blotted for 10 seconds with 10 blot force before plunging..

Rubisco holoenzymes within the native Chlamydomonas pyrenoid. Whole cells were plunge-frozen onto EM grids and then thinned with a focused ion beam instrument.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 5.0 5.077 5.0 6.457 42000. FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF 0 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1 1.5 1.5

Images were collected in movie mode at 17 frames per second

1 D4 BACK PROJECTION 16.5 FSC 0.143 CUT-OFF RELION

The 30,000 subvolumes with the highest template matching cross-correlation scores were used for the final reconstruction. Cumulative electron dose was restricted for the final average by only using the central 60 degrees of the tilt-series (-30 to +30). 16.5 A (FSC 0.143 cut-off) gold-standard resolution. 15.5 A (FSC 0.3 cut-off) cross-resolution of the full dataset to the crystal structure.

30000 1 49828 PDB entry 1GK8, lowpass filtered to 33 A automated template matching and exhaustive extraction PyTom template matching Amira mask segmentation

Template matching hits were filtered with a manually-segmented mask, limiting subvolume extraction to the pyrenoid matrix volume.

IMOD ctfplotter, ctfphaseflip

Defocus of individual tilts was estimated with IMOD's ctfplotter, and CTF correction was performed with ctfphaseflip

166 300. PyTom

46,567 true-positive subvolumes retained; 3,261 false-positive subvolumes discarded. Hierarchical clustering was used to determine which classes to discard (11 out of 166 classes discarded).

NOT APPLICABLE RELION

Angles known from tilt-series acquisition.

emd_3694.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 56 56 56 0 0 0 56 56 56 191.52 191.52 191.52 90.0 90.0 90.0 X Y Z -5.7059126 3.9495337 0.000000003168763 1. 3.42 3.42 3.42 0.5 AUTHOR ::::EMDATABANK.org::::EMD-3694:::: In situ subtomogram average of Rubisco holoenzymes within the pyrenoid of Chlamydomonas reinhardtii. Filtered to 16%u212B. RIGID BODY FIT REAL