6W4F

NMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer nanodisc

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


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


Literature

Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement.

Lee, K.Y., Fang, Z., Enomoto, M., Gasmi-Seabrook, G., Zheng, L., Koide, S., Ikura, M., Marshall, C.B.

(2020) Angew Chem Int Ed Engl 59: 11037-11045

  • DOI: 10.1002/anie.202001758
  • Primary Citation of Related Structures:  
    6W4E, 6W4F

  • PubMed Abstract: 

    • KRAS homo-dimerization has been implicated in the activation of RAF kinases, however, the mechanism and structural basis remain elusive. We developed a system to study KRAS dimerization on nanodiscs using paramagnetic relaxation enhancement (PRE) NMR spectroscopy, and determined distinct structures of membrane-anchored KRAS dimers in the active GTP- and inactive GDP-loaded states ...

    KRAS homo-dimerization has been implicated in the activation of RAF kinases, however, the mechanism and structural basis remain elusive. We developed a system to study KRAS dimerization on nanodiscs using paramagnetic relaxation enhancement (PRE) NMR spectroscopy, and determined distinct structures of membrane-anchored KRAS dimers in the active GTP- and inactive GDP-loaded states. Both dimerize through an α4-α5 interface, but the relative orientation of the protomers and their contacts differ substantially. Dimerization of KRAS-GTP, stabilized by electrostatic interactions between R135 and E168, favors an orientation on the membrane that promotes accessibility of the effector-binding site. Remarkably, "cross"-dimerization between GTP- and GDP-bound KRAS molecules is unfavorable. These models provide a platform to elucidate the structural basis of RAF activation by RAS and to develop inhibitors that can disrupt the KRAS dimerization. The methodology is applicable to many other farnesylated small GTPases.

    Organizational Affiliation: 

    Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apolipoprotein A-IA,
B [auth D]		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
Entity Groups  
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UniProt GroupP02647
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasC [auth B],
D [auth C]		184Homo sapiensMutation(s): 0 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
17F
Query on 17F
Download Ideal Coordinates CCD File 
AB [auth D],
BB [auth D],
CB [auth D],
DB [auth D],
EB [auth D],
AB [auth D],
BB [auth D],
CB [auth D],
DB [auth D],
EB [auth D],
FB [auth D],
GB [auth D],
HC [auth C],
IC [auth C],
R [auth A],
S [auth A],
UB [auth B],
VB [auth B],
WB [auth B],
XB [auth B],
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		 Ligand Interaction
PCW
Query on PCW
Download Ideal Coordinates CCD File 
AA [auth D],
AC [auth C],
BA [auth D],
BC [auth C],
CA [auth D],
AA [auth D],
AC [auth C],
BA [auth D],
BC [auth C],
CA [auth D],
CC [auth C],
DA [auth D],
DC [auth C],
E [auth A],
EA [auth D],
EC [auth C],
F [auth A],
FA [auth D],
FC [auth C],
G [auth A],
GA [auth D],
GC [auth C],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
JB [auth B],
JC [auth C],
K [auth A],
KA [auth D],
KB [auth B],
L [auth A],
LA [auth D],
LB [auth B],
M [auth A],
MA [auth D],
MB [auth B],
N [auth A],
NA [auth D],
NB [auth B],
O [auth A],
OA [auth D],
OB [auth B],
P [auth A],
PA [auth D],
PB [auth B],
Q [auth A],
QA [auth D],
QB [auth B],
RA [auth D],
RB [auth B],
SA [auth D],
SB [auth B],
T [auth A],
TA [auth D],
TB [auth B],
U [auth A],
UA [auth D],
V [auth A],
VA [auth D],
W [auth A],
WA [auth D],
X [auth A],
XA [auth D],
Y [auth D],
YA [auth D],
Z [auth D]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
HB [auth B],
YB [auth C]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
IB [auth B],
ZB [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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View more in-depth experimental data
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: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references