7RSE

NMR-driven structure of the KRAS4B-G12D "alpha-beta" dimer on a lipid bilayer nanodisc


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Oncogenic KRAS G12D mutation promotes dimerization through a second, phosphatidylserine-dependent interface: a model for KRAS oligomerization.

Lee, K.Y.Enomoto, M.Gebregiworgis, T.Gasmi-Seabrook, G.M.C.Ikura, M.Marshall, C.B.

(2021) Chem Sci 12: 12827-12837

  • DOI: https://doi.org/10.1039/d1sc03484g
  • Primary Citation of Related Structures:  
    7RSC, 7RSE

  • PubMed Abstract: 

    KRAS forms transient dimers and higher-order multimers (nanoclusters) on the plasma membrane, which drive MAPK signaling and cell proliferation. KRAS is a frequently mutated oncogene, and while it is well known that the most prevalent mutation, G12D, impairs GTP hydrolysis, thereby increasing KRAS activation, G12D has also been shown to enhance nanoclustering. Elucidating structures of dynamic KRAS assemblies on a membrane has been challenging, thus we have refined our NMR approach that uses nanodiscs to study KRAS associated with membranes. We incorporated paramagnetic relaxation enhancement (PRE) titrations and interface mutagenesis, which revealed that, in addition to the symmetric 'α-α' dimerization interface shared with wild-type KRAS, the G12D mutant also self-associates through an asymmetric 'α-β' interface. The 'α-β' association is dependent on the presence of phosphatidylserine lipids, consistent with previous reports that this lipid promotes KRAS self-assembly on the plasma membrane in cells. Experiments using engineered mutants to spoil each interface, together with PRE probes attached to the membrane or free in solvent, suggest that dimerization through the primary 'α-α' interface releases β interfaces from the membrane promoting formation of the secondary 'α-β' interaction, potentially initiating nanoclustering. In addition, the small molecule BI-2852 binds at a β-β interface, stabilizing a new dimer configuration that outcompetes native dimerization and blocks the effector-binding site. Our data indicate that KRAS self-association involves a delicately balanced conformational equilibrium between transient states, which is sensitive to disease-associated mutation and small molecule inhibitors. The methods developed here are applicable to biologically important transient interactions involving other membrane-associated proteins.


  • Organizational Affiliation

    Department of Medical Biophysics, University of Toronto Toronto Ontario M5G 1L7 Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas
A, B
185Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein A-IC [auth D],
D [auth E]
200Homo sapiensMutation(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
GTEx:  ENSG00000118137 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02647
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
17F (Subject of Investigation/LOI)
Query on 17F

Download Ideal Coordinates CCD File 
AE [auth E]
CA [auth B]
CD [auth E]
DD [auth E]
DF [auth E]
AE [auth E],
CA [auth B],
CD [auth E],
DD [auth E],
DF [auth E],
EB [auth D],
ED [auth E],
FB [auth D],
FF [auth E],
HF [auth E],
IA [auth B],
IC [auth D],
JA [auth B],
L [auth A],
MC [auth E],
NA [auth B],
ND [auth E],
OE [auth E],
PA [auth D],
PB [auth D],
PE [auth E],
QB [auth D],
QC [auth E],
R [auth A],
SC [auth E],
UC [auth E],
VB [auth D],
WB [auth D],
WC [auth E],
XD [auth E],
YA [auth D],
ZA [auth D]
O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
C42 H78 N O10 P
WTBFLCSPLLEDEM-JIDRGYQWSA-N
7Q9 (Subject of Investigation/LOI)
Query on 7Q9

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
AC [auth D]
AD [auth E]
AF [auth E]
AA [auth B],
AB [auth D],
AC [auth D],
AD [auth E],
AF [auth E],
BA [auth B],
BB [auth D],
BC [auth D],
BD [auth E],
BE [auth E],
BF [auth E],
CB [auth D],
CC [auth D],
CE [auth E],
CF [auth E],
DA [auth B],
DB [auth D],
DC [auth D],
DE [auth E],
EA [auth B],
EC [auth D],
EE [auth E],
EF [auth E],
FA [auth B],
FC [auth D],
FD [auth E],
FE [auth E],
G [auth A],
GA [auth B],
GB [auth D],
GC [auth D],
GD [auth E],
GE [auth E],
GF [auth E],
H [auth A],
HA [auth B],
HB [auth D],
HC [auth D],
HD [auth E],
HE [auth E],
I [auth A],
IB [auth D],
ID [auth E],
IE [auth E],
IF [auth E],
J [auth A],
JB [auth D],
JC [auth D],
JD [auth E],
JE [auth E],
JF [auth E],
K [auth A],
KA [auth B],
KB [auth D],
KC [auth D],
KD [auth E],
KE [auth E],
KF [auth E],
LA [auth B],
LB [auth D],
LC [auth D],
LD [auth E],
LE [auth E],
LF [auth E],
M [auth A],
MA [auth B],
MB [auth D],
MD [auth E],
ME [auth E],
N [auth A],
NB [auth D],
NC [auth E],
NE [auth E],
O [auth A],
OA [auth B],
OB [auth D],
OC [auth E],
OD [auth E],
P [auth A],
PC [auth E],
PD [auth E],
Q [auth A],
QA [auth D],
QD [auth E],
QE [auth E],
RA [auth D],
RB [auth D],
RC [auth E],
RD [auth E],
RE [auth E],
S [auth A],
SA [auth D],
SB [auth D],
SD [auth E],
SE [auth E],
T [auth A],
TA [auth D],
TB [auth D],
TC [auth E],
TD [auth E],
TE [auth E],
U [auth A],
UA [auth D],
UB [auth D],
UD [auth E],
UE [auth E],
VA [auth D],
VC [auth E],
VD [auth E],
VE [auth E],
WA [auth D],
WD [auth E],
WE [auth E],
X [auth B],
XA [auth D],
XB [auth D],
XC [auth E],
XE [auth E],
Y [auth B],
YB [auth D],
YC [auth E],
YD [auth E],
YE [auth E],
Z [auth B],
ZB [auth D],
ZC [auth E],
ZD [auth E],
ZE [auth E]
[(2~{R})-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] (~{Z})-octadec-9-enoate
C29 H57 N O8 P
WGQFZGXSOWUAAH-GTPZACKGSA-O
GSP (Subject of Investigation/LOI)
Query on GSP

Download Ideal Coordinates CCD File 
E [auth A],
V [auth B]
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
W [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Other