5B2Z
H-Ras WT in complex with GppNHp (state 2*) before structural transition by humidity control
Summary for 5B2Z
| Entry DOI | 10.2210/pdb5b2z/pdb |
| Related | 5B30 |
| Descriptor | GTPase HRas, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, CALCIUM ION, ... (5 entities in total) |
| Functional Keywords | oncoprotein |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 1 |
| Total formula weight | 19913.30 |
| Authors | Kumasaka, T.,Miyano, N.,Baba, S.,Matsumoto, S.,Kataoka, T.,Shima, F. (deposition date: 2016-02-07, release date: 2016-06-01, Last modification date: 2023-11-08) |
| Primary citation | Matsumoto, S.,Miyano, N.,Baba, S.,Liao, J.,Kawamura, T.,Tsuda, C.,Takeda, A.,Yamamoto, M.,Kumasaka, T.,Kataoka, T.,Shima, F. Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal Sci Rep, 6:25931-25931, 2016 Cited by PubMed Abstract: Ras•GTP adopts two interconverting conformational states, state 1 and state 2, corresponding to inactive and active forms, respectively. However, analysis of the mechanism for state transition was hampered by the lack of the structural information on wild-type Ras state 1 despite its fundamental nature conserved in the Ras superfamily. Here we solve two new crystal structures of wild-type H-Ras, corresponding to state 1 and state 2. The state 2 structure seems to represent an intermediate of state transition and, intriguingly, the state 1 crystal is successfully derived from this state 2 crystal by regulating the surrounding humidity. Structural comparison enables us to infer the molecular mechanism for state transition, during which a wide range of hydrogen-bonding networks across Switch I, Switch II and the α3-helix interdependently undergo gross rearrangements, where fluctuation of Tyr32, translocation of Gln61, loss of the functional water molecules and positional shift of GTP play major roles. The NMR-based hydrogen/deuterium exchange experiments also support this transition mechanism. Moreover, the unveiled structural features together with the results of the biochemical study provide a new insight into the physiological role of state 1 as a stable pool of Ras•GTP in the GDP/GTP cycle of Ras. PubMed: 27180801DOI: 10.1038/srep25931 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.56 Å) |
Structure validation
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