2024-03-13 REL RCSB RCSB RCSB 2017-05-31 2017-08-09 2017-08-09 2024-03-13 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41GM103832 United States GroEL using cryoEM Roh SH Chiu W GroEL, cryoEM, conformational heterogeneity., CHAPERONE Roh SH Hryc CF Jeong HH Fei X Jakana J Lorimer GH Chiu W Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM. Proc. Natl. Acad. Sci. U.S.A. US 114 8259 8264 2017 28710336 doi:10.1073/pnas.1704725114 1091-6490 0040 PNASA6 5w0s FULLOVERLAP Wild type GroEL Wild type GroEL 0 1 Escherichia coli 800 60 kDa chaperonin Escherichia coli 0.05514801999999999 14 Escherichia coli LEVO AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKA NDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTVAVEELKALSVPCSDSKAIAQVGTISANSDETVGKL IAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAK RVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALH ATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP Q6Q099 water 1.8015e-05 107 HOH singleParticle particle 0.1 7.2 ETHANE JEOL 3200FSC FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 1.0 1 D7 3.5 FSC 0.143 CUT-OFF RELION 1.4 37367 COMMON LINE COMMON LINE emd_8750.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 295.2 295.2 295.2 90.0 90.0 90.0 X Y Z -0.11138689 0.20425552 0.00017152682 0.011501166 1.23 1.23 1.23 0.04 AUTHOR GroEL
Regarding negative occupancies: To assess fit-to-density, we derived cross-correlations at the amino acid level and by means of a map/model FSC. To perform this assessment, we generated a weighted map, derived solely from an atomic model that accounted for both ADP of all atoms and weak/negative density of all charged oxygen atoms, and compared it with the experimental map. The weighted map provides a better approximation of the experimental map by simulating map variability as opposed to treating all atoms equally. The correlations for both the FSC and the per-residue assessment showed improvements when properly weighted, further demonstrating that our model provides a good approximation of the experimental data
 emd_8750_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 295.2 295.2 295.2 90.0 90.0 90.0 X Y Z -0.12815152 0.23121184 0.0001777745 0.012761385 1.23 1.23 1.23 AUTHOR GroEL, Conformation 1 emd_8750_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 295.2 295.2 295.2 90.0 90.0 90.0 X Y Z -0.14058115 0.22872394 0.00016871604 0.013656009 1.23 1.23 1.23 AUTHOR GroEL, Conformation 2 emd_8750_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 295.2 295.2 295.2 90.0 90.0 90.0 X Y Z -0.10801727 0.19735506 0.0001694186 0.0110042915 1.23 1.23 1.23 AUTHOR GroEL, Conformation 3