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 3zq1 FULLOVERLAP Non-native RuBisCO substrate protein encapsulated inside the cavity of GroEL capped by GroES with the assistance of nucleotide ATP Non-native RuBisCO substrate protein encapsulated inside the cavity of GroEL capped by GroES with the assistance of nucleotide ATP
The molecule is bullet-shaped
Non-native RuBisCO substrate protein was encapsulated inside the cavity formed by one tetradecamer of GroEL, 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 GroEL-D398A Escherichia coli K-12 BL21 Cytoplasm 0.8 0.8
The D398A mutation prevents ATP hydrolysis by GroEL.
14 Tetradecamer true Escherichia coli BL21(DE3) pACYC P0A6F5 GroES Escherichia coli K-12 Cytoplasm 0.070 0.070 7 Heptamer true Escherichia coli BL21(DE3) 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 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 3200FSC FLOOD BEAM OTHER FIELD EMISSION GUN 300 1.5 5.0 50000.0 70760.0 JEOL 3200FSC CRYOHOLDER 100.9 101.1 101 Objective lens astigmatism was corrected at 100,000 times magnification JEOL 0.0 25.0 2008-12-21 GENERIC GATAN 15 1537 20 8.
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 15.9 OTHER EMAN1 8189
EMAN1
 280 emd_2327.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 -90 -90 -90 180 180 180 381.59998 381.59998 381.59998 90.0 90.0 90.0 X Y Z -0.07791637 1.79304695 0.04864103 0.21416679 2.12 2.12 2.12 1.0 AUTHOR Symmetry-free 3D reconstruction of the bullet-shaped substrate-encapsulated subpopulation sorted from the heterogeneous sample of wild-type GroEL 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