Fig. 2: Different conformational states of the A-loop and 422-loop area. | Nature Communications

Fig. 2: Different conformational states of the A-loop and 422-loop area.

From: Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex

Fig. 2

a (Left) The overview diagram of typical exposed and buried state in KaiC-AA and KaiC-EE. (Right) Corresponding independent exposed and buried state in KaiC-AA and KaiC-EE (denoted as \({S}_{{Ex}1}\), \({S}_{{Ex}2}\), \({S}_{{Bu}1}\), \({S}_{{Bu}2}\), colored in black, royal blue, red, orange, respectively). At the bottom are the close-up view of the A-loop shown in a stick representation superimposed over its corresponding cryo-EM densities in a gray mesh at 3σ, 5σ, 9σ, 9σ level representation, respectively. b The buried state \(\left({S}_{{Bu}1}\right)\) superimposed with previously reported crystal structures in PDB data bank (with 3S1A, 3K0A, 2GBL colored in blue, green and gray, respectively). The A-loop is shown as cartoons without transparency. c A potentially new buried state conformation only found in KaiC-EE data set (denoted as \({S}_{{Bu}3}\), colored in dim gray), with the A-loop and 422-loop densities shown as a gray mesh at 11σ level on the right. d Superimposed the atomic model of \({S}_{{Bu}1}\) and \({S}_{{Bu}3}\), with side chains of M420 and I490 are given in a close-up view and labeled.

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