REL PDBe PDBe PDBe 2013-03-01 2013-03-13 2013-03-13 2014-03-26 Visualizing GroEL/ES in the Act of Encapsulating a Non-Native Substrate Protein Chen D-H Madan D Weaver J Lin Z Schroder GF Chiu W Rye HS protein folding, chaperonin, GroEL, GroEL-GroES, cryo-EM, heterogeneity, substrate, RuBisCO, encapsulation Chen D-H Madan D Weaver J Lin Z Schroder GF Chiu W Rye HS Visualizing GroEL/ES in the act of encapsulating a folding protein. CELL(CAMBRIDGE,MASS.) 153 1354 1365 2013 23746846 doi:10.1016/j.cell.2013.04.052 3zq0 FULLOVERLAP Non-native RuBisCO substrate protein encapsulated inside the cavity of GroEL variant EL43Py capped by GroES with the assistance of nucleotide ATP Non-native RuBisCO substrate protein encapsulated inside the cavity of GroEL variant EL43Py capped by GroES with the assistance of nucleotide ATP
This complex is bullet-shaped
Non-native RuBisCO substrate protein was encapsulated inside the cavity formed by one tetradecamer of GroEL variant EL43Py, one heptamer of GroES and seven nucleotides of ATP 4 0.92 0.92 Estimated by the sum of GroEL molecular weight 800kDa, GroES molecular weight 70kDa and one RuBisCO monomer molecular weight 50kDa GroELcys0-D398A-S43C-pyrene Escherichia coli K-12 Cytoplasm 0.8 0.8
A GroEL variant in which the endogenous Cys residues (138, 458, 519) have been changed to Ala (GroELcys0) was modified to contain two additional mutations: D398A and S43C. The D398A mutation prevents ATP hydrolysis by GroEL, while the S43C mutation, located at the tip of stem loop at the bottom of the GroEL cavity, permits the covalent attachment of N-1-pyrene maleimide to this position.
14 Tetradecamer true Escherichia coli BL21 pACYC P0A6F5 GroES Escherichia coli K-12 0.070 0.070 7 Heptamer true Escherichia coli BL21 pACYC P0A6F9 Ribulose-1,5-bisphosphate carboxylase oxygenase Rhodospirillum rubrum cytoplasm 0.05 0.05
The native RuBisCO is a dimer, but the encapsulated RuBisCO is a non-native monomer.
1 monomer true Escherichia coli BL21(DE3) pUC derived plasmid with T7 promoter Adenosine triphosphate synthetic construct 7 false singleParticle particle 2.4 7.6
50 mM Hepes, 50 mM KOAc, 10 mM Mg(OAc)2, 2 mM DTT
400 mesh R1.2/1.3 Quantifoil grid glow-discharged 10 sec before freezing
 ETHANE 95 98 FEI VITROBOT MARK III Blot for 1 second before plunging JEOL 3000SFF FLOOD BEAM OTHER FIELD EMISSION GUN 300 1.6 1.0 4.7 50000.0 73530.0 OTHER 50 51 50.5 Objective lens astigmatism was corrected at 400,000 times magnification 2008-08-16 GENERIC GATAN 15 2379 30 8. Helium cooled top-entry cartridge
Particle selection was performed semi-automatically using the EMAN1 program, boxer. The contrast transfer function fitting was performed automatically using the program fitctf.py and then fine-tuned manually using the EMAN1 program ctfit. The methodology of EMAN1 multiple-model refinement (EMAN1 program multirefine) for compositionally and conformationally heterogeneous complex analysis was used to sort out the relatively homogeneous bullet-shaped particle images with the substrate protein inside the cis cavity.
Each frame
 C1 OTHER 9.2 OTHER EMAN1 17611
EMAN1
 711 emd_2326.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 -90 -90 -90 180 180 180 367.19998 367.19998 367.19998 90.0 90.0 90.0 X Y Z -0.47194329 2.28602433 0.0433308 0.20919535 2.04 2.04 2.04 1.2 AUTHOR Symmetry-free 3D reconstruction of the bullet-shaped substrate-encapsulated subpopulation sorted from the heterogeneous sample of EL43Py reacted with the substrate protein RuBisCO, GroES and nucleotide ATP
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 1AON A B C D E F G H I J K L M N O P Q R S T U FLEXIBLE FIT DireX cross-correlation coefficient REAL