6PTW

NMR data-driven model of KRas-GMPPNP:RBD-CRD complex tethered to a nanodisc (state B)


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane.

Fang, Z.Lee, K.Y.Huo, K.G.Gasmi-Seabrook, G.Zheng, L.Moghal, N.Tsao, M.S.Ikura, M.Marshall, C.B.

(2020) Proc Natl Acad Sci U S A 117: 12101-12108

  • DOI: https://doi.org/10.1073/pnas.1914076117
  • Primary Citation of Related Structures:  
    6PTS, 6PTW

  • PubMed Abstract: 

    Membrane anchoring of farnesylated KRAS is critical for activation of RAF kinases, yet our understanding of how these proteins interact on the membrane is limited to isolated domains. The RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF engage KRAS and the plasma membrane, unleashing the kinase domain from autoinhibition. Due to experimental challenges, structural insight into this tripartite KRAS:RBD-CRD:membrane complex has relied on molecular dynamics simulations. Here, we report NMR studies of the KRAS:CRAF RBD-CRD complex. We found that the nucleotide-dependent KRAS-RBD interaction results in transient electrostatic interactions between KRAS and CRD, and we mapped the membrane interfaces of the CRD, RBD-CRD, and the KRAS:RBD-CRD complex. RBD-CRD exhibits dynamic interactions with the membrane through the canonical CRD lipid-binding site (CRD β7-8), as well as an alternative interface comprising β6 and the C terminus of CRD and β2 of RBD. Upon complex formation with KRAS, two distinct states were observed by NMR: State A was stabilized by membrane association of CRD β7-8 and KRAS α4-α5 while state B involved the C terminus of CRD, β3-5 of RBD, and part of KRAS α5. Notably, α4-α5, which has been proposed to mediate KRAS dimerization, is accessible only in state B. A cancer-associated mutation on the state B membrane interface of CRAF RBD (E125K) stabilized state B and enhanced kinase activity and cellular MAPK signaling. These studies revealed a dynamic picture of the assembly of the KRAS-CRAF complex via multivalent and dynamic interactions between KRAS, CRAF RBD-CRD, and the membrane.


  • Organizational Affiliation

    Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein A-IA,
B [auth C]
198Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRasC [auth B]185Homo sapiensMutation(s): 0 
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RAF proto-oncogene serine/threonine-protein kinase132Homo sapiensMutation(s): 0 
Gene Names: RAF1RAF
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens)
Explore P04049 
Go to UniProtKB:  P04049
PHAROS:  P04049
GTEx:  ENSG00000132155 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04049
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
17F
Query on 17F

Download Ideal Coordinates CCD File 
AC [auth D]
BC [auth D]
CC [auth D]
GC [auth D]
HC [auth D]
AC [auth D],
BC [auth D],
CC [auth D],
GC [auth D],
HC [auth D],
M [auth A],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth C],
WB [auth D],
XA [auth C],
XB [auth D],
YB [auth D],
ZB [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
PCW
Query on PCW

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth B]
BA [auth C]
BB [auth B]
CA [auth C]
AA [auth C],
AB [auth B],
BA [auth C],
BB [auth B],
CA [auth C],
DA [auth C],
DC [auth D],
E [auth A],
EA [auth C],
EB [auth D],
EC [auth D],
F [auth A],
FA [auth C],
FB [auth D],
FC [auth D],
G [auth A],
GA [auth C],
GB [auth D],
H [auth A],
HA [auth C],
HB [auth D],
I [auth A],
IA [auth C],
IB [auth D],
J [auth A],
JA [auth C],
JB [auth D],
K [auth A],
KA [auth C],
KB [auth D],
L [auth A],
LA [auth C],
LB [auth D],
MA [auth C],
MB [auth D],
N [auth A],
NA [auth C],
NB [auth D],
O [auth A],
OA [auth C],
OB [auth D],
P [auth A],
PA [auth C],
PB [auth D],
Q [auth A],
QA [auth C],
QB [auth D],
R [auth A],
RA [auth C],
RB [auth D],
S [auth A],
SB [auth D],
T [auth C],
TB [auth D],
U [auth C],
UB [auth D],
V [auth C],
VB [auth D],
W [auth C],
X [auth C],
Y [auth C],
YA [auth B],
Z [auth C],
ZA [auth B]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
GNP
Query on GNP

Download Ideal Coordinates CCD File 
CB [auth B]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
IC [auth D],
JC [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DB [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

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: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2020-06-17
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Database references, Other