8EBZ

Crystal Structure of GMPPNP-bound KRAS-G13D mutant at 1.2 Ang resolution

Summary for 8EBZ

• Entry DOI: 10.2210/pdb8ebz/pdb
• Descriptor: Isoform 2B of GTPase KRas, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: kras, k-ras, mutant, cancer, oncoprotein, ras, small gtpase, gmppnp, gppnhp, g13d, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 20022.26

Authors

Chan, A.H.,Simanshu, D.K. (deposition date: 2022-08-31, release date: 2023-06-07, Last modification date: 2024-10-23)

Primary citation

Chao, F.A.,Chan, A.H.,Dharmaiah, S.,Schwieters, C.D.,Tran, T.H.,Taylor, T.,Ramakrishnan, N.,Esposito, D.,Nissley, D.V.,McCormick, F.,Simanshu, D.K.,Cornilescu, G.
Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D .
Commun Biol, 6:594-594, 2023

PubMed Abstract: Localized dynamics of RAS, including regions distal to the nucleotide-binding site, is of high interest for elucidating the mechanisms by which RAS proteins interact with effectors and regulators and for designing inhibitors. Among several oncogenic mutants, methyl relaxation dispersion experiments reveal highly synchronized conformational dynamics in the active (GMPPNP-bound) KRAS, which suggests an exchange between two conformational states in solution. Methyl and P NMR spectra of active KRAS in solution confirm a two-state ensemble interconverting on the millisecond timescale, with a major P atom peak corresponding to the dominant State 1 conformation and a secondary peak indicating an intermediate state different from the known State 2 conformation recognized by RAS effectors. High-resolution crystal structures of active KRAS and KRAS-RAF1 RBD complex provide snapshots of the State 1 and 2 conformations, respectively. We use residual dipolar couplings to solve and cross-validate the structure of the intermediate state of active KRAS, showing a conformation distinct from those of States 1 and 2 outside the known flexible switch regions. The dynamic coupling between the conformational exchange in the effector lobe and the breathing motion in the allosteric lobe is further validated by a secondary mutation in the allosteric lobe, which affects the conformational population equilibrium.

PubMed: 37268708
DOI: 10.1038/s42003-023-04960-6

Experimental method

X-RAY DIFFRACTION (1.2 Å)