6W4E | pdb_00006w4e

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

PDB DOI: https://doi.org/10.2210/pdb6W4E/pdb
BMRB: 30734

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2020-03-10 Released: 2020-04-15
Deposition Author(s): Lee, K., Fang, Z., Enomoto, M., Gasmi-Seabrook, G.M., Zheng, L., Marshall, C.B., Ikura, M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 3000
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

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

PubMed: 32227412 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202001758
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 152.84 kDa
Atom Count: 10,576
Modeled Residue Count: 764
Deposited Residue Count: 770
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apolipoprotein A-I	A, B [auth D]	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 GTEx: ENSG00000118137
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02647
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	C [auth B], D [auth C]	185	Homo sapiens	Mutation(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 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
17F Query on 17F Download:Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain DC [auth C] SDF format, chain EB [auth D] SDF format, chain EC [auth C] SDF format, chain FB [auth D] SDF format, chain FC [auth C] SDF format, chain IC [auth C] SDF format, chain JC [auth C] SDF format, chain OB [auth B] SDF format, chain PB [auth B] SDF format, chain QB [auth B] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain Z [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain DC [auth C] MOL2 format, chain EB [auth D] MOL2 format, chain EC [auth C] MOL2 format, chain FB [auth D] MOL2 format, chain FC [auth C] MOL2 format, chain IC [auth C] MOL2 format, chain JC [auth C] MOL2 format, chain OB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain QB [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain DC [auth C] mmCIF format, chain EB [auth D] mmCIF format, chain EC [auth C] mmCIF format, chain FB [auth D] mmCIF format, chain FC [auth C] mmCIF format, chain IC [auth C] mmCIF format, chain JC [auth C] mmCIF format, chain OB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain QB [auth B] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain Z [auth A]	BB [auth D] CB [auth D] DB [auth D] DC [auth C] EB [auth D] BB [auth D], CB [auth D], DB [auth D], DC [auth C], EB [auth D], EC [auth C], FB [auth D], FC [auth C], IC [auth C], JC [auth C], OB [auth B], PB [auth B], QB [auth B], S [auth A], T [auth A], Z [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		Interactions Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain DC [auth C] Focus chain EB [auth D] Focus chain EC [auth C] Focus chain FB [auth D] Focus chain FC [auth C] Focus chain IC [auth C] Focus chain JC [auth C] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth A]
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth D] SDF format, chain AC [auth C] SDF format, chain BA [auth D] SDF format, chain BC [auth C] SDF format, chain CA [auth D] SDF format, chain CC [auth C] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain GC [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain HC [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain IB [auth B] SDF format, chain JA [auth D] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MB [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain NB [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain TB [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth D] SDF format, chain UB [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth D] SDF format, chain VB [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth D] SDF format, chain WB [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth D] SDF format, chain XB [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth D] SDF format, chain YB [auth C] SDF format, chain ZA [auth D] SDF format, chain ZB [auth C] SDF format, chain J [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain AC [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain BC [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain CC [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain GC [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain HC [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain UB [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain VB [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain WB [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain XB [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain YB [auth C] MOL2 format, chain ZA [auth D] MOL2 format, chain ZB [auth C] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain AC [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain BC [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain CC [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain GC [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain HC [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain NB [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain TB [auth C] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain UB [auth C] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain VB [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth D] mmCIF format, chain WB [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth D] mmCIF format, chain XB [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth D] mmCIF format, chain YB [auth C] mmCIF format, chain ZA [auth D] mmCIF format, chain ZB [auth C] mmCIF format, chain J [auth A]	AA [auth D] AB [auth D] AC [auth C] BA [auth D] BC [auth C] AA [auth D], AB [auth D], AC [auth C], BA [auth D], BC [auth C], CA [auth D], CC [auth C], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], GC [auth C], H [auth A], HA [auth D], HC [auth C], I [auth A], IA [auth D], IB [auth B], J [auth A], JA [auth D], JB [auth B], 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], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], SA [auth D], TA [auth D], TB [auth C], U [auth A], UA [auth D], UB [auth C], V [auth A], VA [auth D], VB [auth C], W [auth A], WA [auth D], WB [auth C], X [auth A], XA [auth D], XB [auth C], Y [auth A], YA [auth D], YB [auth C], ZA [auth D], ZB [auth C]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain AA [auth D] Focus chain AB [auth D] Focus chain AC [auth C] Focus chain BA [auth D] Focus chain BC [auth C] Focus chain CA [auth D] Focus chain CC [auth C] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain GC [auth C] Focus chain H [auth A] Focus chain HA [auth D] Focus chain HC [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth D] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth D] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth D] Focus chain WB [auth C] Focus chain X [auth A] Focus chain XA [auth D] Focus chain XB [auth C] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain YB [auth C] Focus chain ZA [auth D] Focus chain ZB [auth C]
GSP Query on GSP Download:Ideal Coordinates CCD File SDF format, chain GB [auth B] SDF format, chain RB [auth C] MOL2 format, chain GB [auth B] MOL2 format, chain RB [auth C] mmCIF format, chain GB [auth B] mmCIF format, chain RB [auth C]	GB [auth B], RB [auth C]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ S XOFLBQFBSOEHOG-UUOKFMHZSA-N		Interactions Focus chain GB [auth B] Focus chain RB [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain HB [auth B] SDF format, chain SB [auth C] MOL2 format, chain HB [auth B] MOL2 format, chain SB [auth C] mmCIF format, chain HB [auth B] mmCIF format, chain SB [auth C]	HB [auth B], SB [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain HB [auth B] Focus chain SB [auth C]