2018-08-22 REL PDBj PDBj PDBj 2017-05-10 2018-06-13 2018-06-13 2018-08-22 Folding intermediate of RuBisCO in complex with the GroEL chaperonin. Class3. Natesh R Clare DK Farr GW Horwich AL Saibil HR Natesh R Clare DK Farr GW Horwich AL Saibil HR A two-domain folding intermediate of RuBisCO in complex with the GroEL chaperonin. Int. J. Biol. Macromol. UK 118 671 675 2018 29959019 doi:10.1016/j.ijbiomac.2018.06.120 1879-0003 0708 IJBMDR EMD-6727 associated EM volume EMD-6725 other EM volume EMD-6726 other EM volume Non-native RuBisCO in complex with chaperonin GroEL Non-native RuBisCO in complex with chaperonin GroEL 0 1
Apo GroEL.D473C.His6 with unbound RuBisCO folding intermediate as seen in 3D reconstruction for Class3. Only GroEL region was observed in EM map.
Escherichia coli Escherichia coli 0.812 GroEL Escherichia coli
GroEL.D473C.His6 Tetradecamer
Escherichia coli LEVO AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTVAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLIIAEDVEGEALATAVVNTIRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGCGNYGYNAATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP 3.6.4.9 singleParticle particle 0.0863 7.5 50.0 HEPES 10.0 KOAc Pottasium Acetate 10.0 Mg(OAc)2 Magnesium Acetate 10.0 DTT DTT
Folding Buffer (FB) consists of 50 mM HEPES pH7.5, 10 mM KOAc, 10 mM Mg(OAc)2, 10 mM DTT. RuBisCO denatured in 20mM HCl, 10 M Urea, 20 mM DTT
 Protochips Inc., USA COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR
The C-flat holey grids were coated with thin home made carbon film.
 ETHANE 298 HOMEMADE PLUNGER
Blot approx. 1 sec before plunging. Visual..
RuBisCO denatured in acid urea was complexed with GroEL.D473C.His6 in Folding Buffer. This entry Class3 contains Apo GroEL and hence its real molecular weight would be be 0.812 M Da. Hence the real concentration of 1 uM would be actually 0.0812 mg/mL.
 FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 40.0 2.0 1.0 3.5 50000. 50000. GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN 100.0 100.0 KODAK SO-163 FILM 7.0 11 468 1.0 10.0
Images were collected on Kodak SO-163 Film. Dose was 10-15 e-/A2/sec.
 1
For the binary complex data sets, the positions of particles were noted in MRC programme XIMDISP. Perl script was used to extract particles in boxes of 512 x 512 pixels using the MRC program LABEL, and phase corrected using SPIDER. After CTF correction, the box size was cropped and sampling reduced so that all images were at 2.8 A per pixel in 196 x 196 pixel boxes. Images were band-pass filtered between 285 A and 6 A and normalized to zero mean and the same sigma in SPIDER.
15477
15477 particles were used in image processing after pruning bad particles in the dataset. 3 classes were obtained. This reconstruction is class 3 with non-native RuBisCO un-bound to GroELD473C.His6.
 ctffind3, label and spider
CTF phase flipping was perfomed
An image of side view generated from a 30 A filtered empty GroEL EM map previously constructed within the lab.
 3 C1 BACK PROJECTION 11.0 FSC 0.5 CUT-OFF SPIDER
In 3D reconstruction for Class 3: Resolution is 9 A for C7 symmetrised map after iteration cycle 7. Resolution is 11 A for asymmetric C1 reconstruction after iteration cycle 13.
6003 ANGULAR RECONSTITUTION IMAGIC
ANCHOR SET
 PROJECTION MATCHING 260 CC 2.0 SPIDER 3 5000. IMAGIC
approximately 5000 in each class, with total 15477 particles in total.
 emd_6727.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 196 196 196 0 0 0 196 196 196 548.8 548.8 548.8 90.0 90.0 90.0 X Y Z -0.70907927 9.996134 0.016255789 0.23185983 2.8 2.8 2.8 0.25 AUTHOR Folding intermediate of RuBisCO in complex with the GroEL chaperonin. Class3. 1OEL 2-525 RIGID BODY FIT
Rigid body fit