5B2Z image
Deposition Date 2016-02-07
Release Date 2016-06-01
Last Version Date 2023-11-08
Entry Detail
PDB ID:
5B2Z
Keywords:
Title:
H-Ras WT in complex with GppNHp (state 2*) before structural transition by humidity control
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.56 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
H 3 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:GTPase HRas
Gene (Uniprot):HRAS
Chain IDs:A
Chain Length:171
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal
Sci Rep 6 25931 25931 (2016)
PMID: 27180801 DOI: 10.1038/srep25931

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures