9C1A | pdb_00009c1a

Crystal structure of GDP-bound human M-RAS protein in crystal form I

• PDB DOI: https://doi.org/10.2210/pdb9C1A/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-28 Released: 2024-09-11 
• Deposition Author(s): Bester, S.M., Abrahamsen, R., Samora, L.R., Wu, W.-I., Mou, T.-C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the GDP-bound human M-RAS protein in two crystal forms.

Bester, S.M., Abrahamsen, R., Rodrigues Samora, L., Wu, W.I., Mou, T.C.

(2024) Acta Crystallogr F Struct Biol Commun 80: 220-227

• PubMed: 39196705 
• DOI: https://doi.org/10.1107/S2053230X24007969
• Primary Citation Related Structures: 
  9C1A, 9C1B


• PubMed Abstract: 
  

  M-RAS plays a crucial role in the RAF-MEK signaling pathway. When activated by GTP, M-RAS forms a complex with SHOC2 and PP1C, initiating downstream RAF-MEK signal transduction. In this study, the crystal structure of the GDP-bound human M-RAS protein is presented with two forms of crystal packing. Both the full-length and truncated human M-RAS structures aligned well with the high-confidence section of the AlphaFold2-predicted structure with low r.m.s.d., except for the Switch regions. Despite high sequence similarity to the available mouse M-RAS structure, the full-length human M-RAS structure exhibits unique crystal packing. This inactive human M-RAS structure could offer novel insights for the design of selective compounds targeting M-RAS.

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Organizational Affiliation: 
• Pfizer Boulder Research and Development, 3200 Walnut Street, Boulder, CO 80301, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.02 kDa 
• Atom Count: 1,632 
• Modeled Residue Count: 167 
• Deposited Residue Count: 193 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein M-Ras	A	193	Homo sapiens	Mutation(s): 0  Gene Names: MRAS, RRAS3 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O14807 (Homo sapiens) Explore O14807  Go to UniProtKB:  O14807
PHAROS:  O14807 GTEx:  ENSG00000158186

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.653	α = 90
b = 108.653	β = 90
c = 65.759	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Bester, S.M., Abrahamsen, R., Samora, L.R., Wu, W.-I., Mou, T.-C.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2024-09-18
  Changes: Database references