2MSC

NMR data-driven model of GTPase KRas-GDP tethered to a lipid-bilayer nanodisc

• PDB DOI:  https://doi.org/10.2210/pdb2MSC/pdb
• BMRB: 25114

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-29 Released: 2015-06-03 
• Deposition Author(s): Mazhab-Jafari, M., Stathopoulos, P., Marshall, C., Ikura, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 3000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site.

Mazhab-Jafari, M.T., Marshall, C.B., Smith, M.J., Gasmi-Seabrook, G.M., Stathopulos, P.B., Inagaki, F., Kay, L.E., Neel, B.G., Ikura, M.

(2015) Proc Natl Acad Sci U S A 112: 6625-6630

• PubMed: 25941399 
• DOI: https://doi.org/10.1073/pnas.1419895112
• Primary Citation of Related Structures:  
  2MSC, 2MSD, 2MSE


• PubMed Abstract: 
  

K-RAS4B (Kirsten rat sarcoma viral oncogene homolog 4B) is a prenylated, membrane-associated GTPase protein that is a critical switch for the propagation of growth factor signaling pathways to diverse effector proteins, including rapidly accelerated fibrosarcoma (RAF) kinases and RAS-related protein guanine nucleotide dissociation stimulator (RALGDS) proteins. Gain-of-function KRAS mutations occur frequently in human cancers and predict poor clinical outcome, whereas germ-line mutations are associated with developmental syndromes. However, it is not known how these mutations affect K-RAS association with biological membranes or whether this impacts signal transduction. Here, we used solution NMR studies of K-RAS4B tethered to nanodiscs to investigate lipid bilayer-anchored K-RAS4B and its interactions with effector protein RAS-binding domains (RBDs). Unexpectedly, we found that the effector-binding region of activated K-RAS4B is occluded by interaction with the membrane in one of the NMR-observable, and thus highly populated, conformational states. Binding of the RAF isoform ARAF and RALGDS RBDs induced marked reorientation of K-RAS4B from the occluded state to RBD-specific effector-bound states. Importantly, we found that two Noonan syndrome-associated mutations, K5N and D153V, which do not affect the GTPase cycle, relieve the occluded orientation by directly altering the electrostatics of two membrane interaction surfaces. Similarly, the most frequent KRAS oncogenic mutation G12D also drives K-RAS4B toward an exposed configuration. Further, the D153V and G12D mutations increase the rate of association of ARAF-RBD with lipid bilayer-tethered K-RAS4B. We revealed a mechanism of K-RAS4B autoinhibition by membrane sequestration of its effector-binding site, which can be disrupted by disease-associated mutations. Stabilizing the autoinhibitory interactions between K-RAS4B and the membrane could be an attractive target for anticancer drug discovery.

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Organizational Affiliation: 

Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada M5G 2M9; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 131.18 kDa 
• Atom Count: 9,072 
• Modelled Residue Count: 581 
• Deposited Residue Count: 587 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apolipoprotein A-I	A, B [auth C]	200	Homo sapiens	Mutation(s): 0  Gene Names: APOA1
UniProt & NIH Common Fund Data Resources
Find proteins for P02647 (Homo sapiens) Explore P02647  Go to UniProtKB:  P02647
PHAROS:  P02647

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	C [auth B]	187	Homo sapiens	Mutation(s): 0  Gene Names: KRAS, KRAS2, RASK2, hCG_14731
UniProt
Find proteins for A0A024RAV5 (Homo sapiens) Explore A0A024RAV5  Go to UniProtKB:  A0A024RAV5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
17F	AC [auth A], BC [auth A], CC [auth A], DC [auth A], EC [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], XB [auth A], YB [auth A], ZB [auth A]	O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine C42 H78 N O10 P WTBFLCSPLLEDEM-JIDRGYQWSA-N
PCW	AA [auth A], AB [auth A], BA [auth A], BB [auth A], CA [auth A], CB [auth A], D [auth A], DA [auth A], DB [auth A], E [auth A], EA [auth A], EB [auth A], F [auth A], FA [auth A], FB [auth A], G [auth A], GA [auth A], GB [auth A], H [auth A], HA [auth A], HB [auth A], I [auth A], IA [auth A], IB [auth A], J [auth A], JB [auth A], K [auth A], KB [auth A], L [auth A], LB [auth A], M [auth A], MB [auth A], N [auth A], NB [auth A], O [auth A], OB [auth A], P [auth A], PB [auth A], Q [auth A], QB [auth A], R [auth A], RA [auth A], RB [auth A], S [auth A], SA [auth A], SB [auth A], T [auth A], TA [auth A], TB [auth A], U [auth A], UA [auth A], UB [auth A], V [auth A], VA [auth A], VB [auth A], W [auth A], WA [auth A], WB [auth A], X [auth A], XA [auth A], Y [auth A], YA [auth A], Z [auth A], ZA [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H85 N O8 P SNKAWJBJQDLSFF-NVKMUCNASA-O
GDP	FC [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	GC [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 3000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Mazhab-Jafari, M., Stathopoulos, P., Marshall, C., Ikura, M.

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-06-10
  Changes: Database references
• Version 1.2: 2019-12-11
  Changes: Data collection, Database references, Experimental preparation, Source and taxonomy, Structure summary