Primary Citation PubMed: 16288915
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Biomolecular pleiomorphism probed by spatial interpolation of coarse models.
(2008) Bioinformatics 24
PubMed: 18757874 | PubMedCentral: PMC2732278 | DOI: 10.1093/bioinformatics/btn461
The rigid body docking of the complex identified the locations of the 14 monomers (PDB entry 1xck; Berman et al. , 2000 ) in the 3D map, and emphasized the conformational differences in the datasets (... Fig. 2 B).
Publication Year: 2008
Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.
(2011) PLoS Comput Biol 7
PubMed: 21423709 | PubMedCentral: PMC3053311 | DOI: 10.1371/journal.pcbi.1002004
A total of 21 crystal structures (287 GroEL subunits) were kept for further analysis (PDB-codes: 1PCQ, 1PF9, 1SVT, 3C9V, 1AON, 1GRU, 1MNF, 1XCK, 2C7D, 2NWC, 3E76, 2EU1, 1SS8, 1SX3, 1J4Z, 1KPO, 2C7E, 1... P8, 1OEL, 1WE3, 1WF4).
The atomic models were prepared from the high-resolution crystal structures with PDB codes 1XCK chain A  and 1SVT chain A  , for the closed and open forms, respectively.
Contact matrices were calculated for 28 closed (T) apo subunits (PDB code: 1XCK, 1SS8, 1OEL), 28 closed (T) ATP bound subunits (PDB code: 1KP8, 1SX3) and 28 open (R″) ADP bound subunits (PDB codes: 1AON, 1SVT, 1SX4, and 1PF9), and 6000 snapshots obtained from the last 50 ns of the 12 independent MD simulations on the closed GroEL subunit (6 apo and 6 holo).
The RMSd between the open and closed X-ray structure (PDB ids: 1SVT and 1XCK, respectively) is 12.30 Å.
Publication Year: 2011
A Bayesian view on cryo-EM structure determination.
(2012) J Mol Biol 415
PubMed: 22100448 | PubMedCentral: PMC3314964 | DOI: 10.1016/j.jmb.2011.11.010
The calculation of FSC curves between these maps and a fitted 2.9-Å GroEL crystal structure (Protein Data Bank ID: 1XCK , see Experimental Procedures ) confirmed that MAP refinement had reache... a higher resolution than the conventional approach ( Fig. 3 a, continuous lines).
The true resolution of the GroEL reconstructions was assessed by FSC with a published crystal structure (Protein Data Bank ID: 1XCK ).
Publication Year: 2012
RELION: implementation of a Bayesian approach to cryo-EM structure determination.
(2012) J Struct Biol 180
PubMed: 23000701 | PubMedCentral: PMC3690530 | DOI: 10.1016/j.jsb.2012.09.006
Reconstruction quality was assessed by FSC calculations between the reconstructed maps and a symmetrized GroEL crystal structure (PDB-ID 1XCK ) ( Bartolucci et al., 2005 ) that was also used to assess... GroEL reconstructions in a previous study ( Scheres, 2012 ).
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