7OGF

GTPase HRAS mutant D33K under 900 MPa pressure

PDB DOI: 10.2210/pdb7OGF/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2021-05-06 Released: 2022-02-09
Deposition Author(s): Colloc'h, N.C., Girard, E., Prange, T., Kalbitzer, H.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.333
R-Value Work: 0.242
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography.

Girard, E., Lopes, P., Spoerner, M., Dhaussy, A.C., Prange, T., Kalbitzer, H.R., Colloc'h, N.

(2022) Chem Sci 13: 2001-2010

PubMed: 35308861 Search on PubMedSearch on PubMed Central
DOI: 10.1039/d1sc05488k
Primary Citation of Related Structures:
7OG9, 7OGA, 7OGB, 7OGC, 7OGD, 7OGE, 7OGF

PubMed Abstract:

In this work, we experimentally investigate the allosteric transitions between conformational states on the Ras oncogene protein using high pressure crystallography. Ras protein is a small GTPase involved in central regulatory processes occurring in multiple conformational states. Ras acts as a molecular switch between active GTP-bound, and inactive GDP-bound states, controlling essential signal transduction pathways. An allosteric network of interactions between the effector binding regions and the membrane interacting regions is involved in Ras cycling. The conformational states which coexist simultaneously in solution possess higher Gibbs free energy than the ground state. Equilibria between these states can be shifted by applying pressure favouring conformations with lower partial molar volume, and has been previously analyzed by high-pressure NMR spectroscopy. High-pressure macromolecular crystallography (HPMX) is a powerful tool perfectly complementary to high-pressure NMR, allowing characterization at the molecular level with a high resolution the different allosteric states involved in the Ras cycling. We observe a transition above 300 MPa in the crystal leading to more stable conformers. Thus, we compare the crystallographic structures of Ras(wt)·Mg ²⁺·GppNHp and Ras(D33K)·Mg ²⁺·GppNHp at various high hydrostatic pressures. This gives insight into per-residue descriptions of the structural plasticity involved in allosteric equilibria between conformers. We have mapped out at atomic resolution the different segments of Ras protein which remain in the ground-state conformation or undergo structural changes, adopting excited-energy conformations corresponding to transient intermediate states. Such in crystallo phase transitions induced by pressure open the possibility to finely explore the structural determinants related to switching between Ras allosteric sub-states without any mutations nor exogenous partners.

Organizational Affiliation:

ISTCT UMR 6030, CNRS, Université de Caen Normandie, CERVOxy Group, Centre Cyceron Caen France colloch@cyceron.fr.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	A	166	Homo sapiens	Mutation(s): 1 Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112 Go to UniProtKB: P01112
PHAROS: P01112
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01112
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP (Subject of Investigation/LOI) Query on GNP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Ligand Interaction
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Ligand Interaction
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A]	D [auth A], F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction