6PTS | pdb_00006pts

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

PDB DOI: https://doi.org/10.2210/pdb6PTS/pdb
BMRB: 30639

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-16 Released: 2020-05-13
Deposition Author(s): Fang, Z., Lee, K., Gasmi-Seabrook, G., Ikura, M., Marshall, C.B.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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 1.4 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

PubMed: 32414921 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1914076117
Primary Citation 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

Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada.

Macromolecule Content

Total Structure Weight: 146.21 kDa
Atom Count: 10,142
Modeled Residue Count: 713
Deposited Residue Count: 713
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apolipoprotein A-I	A, B [auth C]	198	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]	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

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RAF proto-oncogene serine/threonine-protein kinase	D	132	Homo sapiens	Mutation(s): 0 Gene Names: RAF1, RAF EC: 2.7.11.1
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04049
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
17F Query on 17F Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain CC [auth D] SDF format, chain DC [auth D] SDF format, chain EC [auth D] SDF format, chain FC [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NB [auth B] SDF format, chain OB [auth B] SDF format, chain PB [auth B] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain CC [auth D] MOL2 format, chain DC [auth D] MOL2 format, chain EC [auth D] MOL2 format, chain FC [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain OB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain CC [auth D] mmCIF format, chain DC [auth D] mmCIF format, chain EC [auth D] mmCIF format, chain FC [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth B] mmCIF format, chain OB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	AB [auth C] CC [auth D] DC [auth D] EC [auth D] FC [auth D] AB [auth C], CC [auth D], DC [auth D], EC [auth D], FC [auth D], M [auth A], N [auth A], NB [auth B], OB [auth B], PB [auth B], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	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 AB [auth C] Focus chain CC [auth D] Focus chain DC [auth D] Focus chain EC [auth D] Focus chain FC [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AC [auth D] SDF format, chain BA [auth C] SDF format, chain BB [auth B] SDF format, chain BC [auth D] SDF format, chain CA [auth C] SDF format, chain CB [auth B] SDF format, chain DA [auth C] SDF format, chain DB [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain EB [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain FB [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain GB [auth B] SDF format, chain GC [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain HB [auth B] SDF format, chain HC [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain LB [auth B] SDF format, chain MA [auth C] SDF format, chain MB [auth B] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain SB [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain TB [auth D] SDF format, chain U [auth A] SDF format, chain UB [auth D] SDF format, chain V [auth C] SDF format, chain VB [auth D] SDF format, chain W [auth C] SDF format, chain WB [auth D] SDF format, chain X [auth C] SDF format, chain XB [auth D] SDF format, chain Y [auth C] SDF format, chain YB [auth D] SDF format, chain Z [auth C] SDF format, chain ZB [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain AC [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth B] MOL2 format, chain GC [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth B] MOL2 format, chain HC [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UB [auth D] MOL2 format, chain V [auth C] MOL2 format, chain VB [auth D] MOL2 format, chain W [auth C] MOL2 format, chain WB [auth D] MOL2 format, chain X [auth C] MOL2 format, chain XB [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain YB [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain ZB [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain AC [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth B] mmCIF format, chain BC [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth B] mmCIF format, chain GC [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth B] mmCIF format, chain HC [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain MB [auth B] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain SB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain TB [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UB [auth D] mmCIF format, chain V [auth C] mmCIF format, chain VB [auth D] mmCIF format, chain W [auth C] mmCIF format, chain WB [auth D] mmCIF format, chain X [auth C] mmCIF format, chain XB [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain YB [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain ZB [auth D]	AA [auth C] AC [auth D] BA [auth C] BB [auth B] BC [auth D] AA [auth C], AC [auth D], BA [auth C], BB [auth B], BC [auth D], CA [auth C], CB [auth B], DA [auth C], DB [auth B], E [auth A], EA [auth C], EB [auth B], F [auth A], FA [auth C], FB [auth B], G [auth A], GA [auth C], GB [auth B], GC [auth D], H [auth A], HA [auth C], HB [auth B], HC [auth D], I [auth A], IA [auth C], IB [auth B], J [auth A], JA [auth C], JB [auth B], K [auth A], KA [auth C], KB [auth B], L [auth A], LA [auth C], LB [auth B], MA [auth C], MB [auth B], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], SB [auth D], T [auth A], TA [auth C], TB [auth D], U [auth A], UB [auth D], V [auth C], VB [auth D], W [auth C], WB [auth D], X [auth C], XB [auth D], Y [auth C], YB [auth D], Z [auth C], ZB [auth D]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain AA [auth C] Focus chain AC [auth D] Focus chain BA [auth C] Focus chain BB [auth B] Focus chain BC [auth D] Focus chain CA [auth C] Focus chain CB [auth B] Focus chain DA [auth C] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EA [auth C] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FA [auth C] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GA [auth C] Focus chain GB [auth B] Focus chain GC [auth D] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth B] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth B] Focus chain MA [auth C] Focus chain MB [auth B] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UB [auth D] Focus chain V [auth C] Focus chain VB [auth D] Focus chain W [auth C] Focus chain WB [auth D] Focus chain X [auth C] Focus chain XB [auth D] Focus chain Y [auth C] Focus chain YB [auth D] Focus chain Z [auth C] Focus chain ZB [auth D]
GNP Query on GNP Download:Ideal Coordinates CCD File SDF format, chain QB [auth B] MOL2 format, chain QB [auth B] mmCIF format, chain QB [auth B]	QB [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain QB [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain IC [auth D] SDF format, chain JC [auth D] MOL2 format, chain IC [auth D] MOL2 format, chain JC [auth D] mmCIF format, chain IC [auth D] mmCIF format, chain JC [auth D]	IC [auth D], JC [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain IC [auth D] Focus chain JC [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain RB [auth B] MOL2 format, chain RB [auth B] mmCIF format, chain RB [auth B]	RB [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain RB [auth B]