Cryo-EM structure of the plant actin filaments from Zea mays pollen

2024-03-27 REL PDBj PDBj PDBj 2018-11-28 2019-11-06 2019-11-06 2024-03-27 National Natural Science Foundation of China 91854206 China National Natural Science Foundation of China 31770206 China National Natural Science Foundation of China 31770794 China Ministry of Science and Technology (China) 2013CB126902 China Ministry of Science and Technology (China) 2017YFA0504700 China Cryo-EM structure of the plant actin filaments from Zea mays pollen Ren ZH Zhang Y Microfilament, Helix, Actin, PROTEIN FIBRIL Ren Z Zhang Y Zhang Y He Y Du P Wang Z Sun F Ren H Cryo-EM Structure of Actin Filaments fromZea maysPollen. Plant Cell US 31 2855 2867 2019 31628168 doi:10.1105/tpc.18.00973 1532-298X 2109 PLCEEW 6iug FULLOVERLAP The actin filament from Zea mays pollen The actin filament from Zea mays pollen 0 1

Plant actin was purified from the pollen which was collected from maize (Zea mays) plants and polymerized at room temperature for 4 hours.

Zea mays Pollen grains 15 pollen F-actin Zea mays pollen grains 0.041211120999999996 5 LEVO IQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEAQSKRGILTLKYPIEHGIVSNWDDMEK IWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVP IYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDMKEKLAYIALDYDQEMETAKTSSSVEKSYELPD GQVITIGAERFRCPEVLFQPSFIGMEAAGIHETTYNSIMKCDVDIRKDLYGNIVLSGGTTMFPGIADRMSKEITALAPSS MKIKVVAPPERKYSVWIGGSILASLSTFQQMWIAKAEYDESGPSIVHRKCF B6TQ08 ADENOSINE-5'-DIPHOSPHATE 0.000427201 5 ADP MAGNESIUM ION 2.4305e-05 5 MG helical filament 0.4 7.0 5.0 Tris 0.01 NaN3 0.5 DTT 0.2 ATP 50.0 KCl 1.0 MgCl2 0.8 EGTA 10.0 imidazole COPPER 400 CARBON HOLEY GLOW DISCHARGE 60 OTHER ETHANE 100.0 298.0 FEI VITROBOT MARK IV

Blotting time of 5.5 s and blotting force of level 2.

Plant actin was dialyzed against buffer solution with pH 7.0 overnight in order to change the alkaline pH to the neutral pH and then polymerized at the final concentration of 0.4 mg/mL.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.2 2.0 22500.0 22013.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 7676 7420 2-27 3605 5.44 39.0

A total of 3,605 micrographs were recorded at a calibrated pixel size of 1.063 angstrom.

The micrographs such as those with pollutions, bad Thon rings, large defocus values and others, were excluded before filament boxing. 1,540 micrographs were finally sorted out as "good" ones.

5100 27.5 -166.77 C1 BACK PROJECTION 3.9 FSC 0.143 CUT-OFF SPIDER 24.08 35684 40943 SPIDER 24.08 Spider script was used to generate actin segments

A total of 8,609 ZMPA filaments were boxed using e2helixboxer.py in the package of EMAN2 with box width 168 and 77% box-overlap. A total of 40,943 segments were generated with box-size of 384.

A cylinder with diamter the same as plant actin was generated by Spider and used as starting model

NOT APPLICABLE SPIDER 24.08

Euler angles were assigned by cross correlation calcualtion of projection matching between projections of the model generated from last iteration and the images.

emd_9734.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 -100 -100 -100 200 200 200 212.59999 212.59999 212.59999 90.0 90.0 90.0 X Y Z -0.00038637855 0.0008742896 -0.000039204464 0.00007096263 1.063 1.063 1.063 0.000291 AUTHOR ::::EMDATABANK.org::::EMD-9734:::: None 5OOC C PDB experimental model RIGID BODY FIT

Chain C from pdb 5OOC was rigid body fitted to plant actin map using Chimera; Then Phenix was used for real space refinement. Finally, filament with 5 real space refinement units were generated using helical parameter, and this filament with 5 units was real space refined using Phenix again.

Correlation coefficient RECIPROCAL 70.0