6VJJ: Wild-type KRAS4b

Crystal Structure of wild-type KRAS4b (GMPPNP-bound) in complex with RAS-binding domain (RBD) of RAF1/CRAF. Determined by X-ray diffraction at 1.4 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,222
Mol. weight: 29.33 kDa
Ligands: MG, GNP
Released: 25 Nov 2020

Explore 6VJJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VJJ contains 11 α-helices and 13 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	62-64	3
α-helix	65-74	10
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
α-helix	152-166	15

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	57-61	5	1
β-strand	67-71	5	1
β-strand	77	1	2
α-helix	78-88	11
α-helix	93-95	3
β-strand	96-100	5	1
α-helix	108-109	2
β-strand	110-111	2	1
β-strand	117	1	2
α-helix	118-121	4
β-strand	125-130	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTPase KRas	A	protein	170	Homo sapiens	P01116 (AlphaFold model)
RAF proto-oncogene serine/threonine-protein kinase	B	protein	80	Homo sapiens	P04049 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VJJ_1 GTPase KRas (chains A)
GMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTA
GQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCD
LPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

Sequence of entity 2 (B), FASTA

>6VJJ_2 RAF proto-oncogene serine/threonine-protein kinase (chains B)
SKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKAR
LDWNTDAASLIGEELQVDFL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

Water and common crystallization additives (CL, EDO, MPD) are not listed.

Primary citation

KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation. Tran, T.H., Chan, A.H., Young, L.C. et al. Nat Commun (2021) 12:1176-1176. DOI 10.1038/s41467-021-21422-x · PubMed

Other PDB entries of the same protein (UniProt P01116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9IAY 0.95 Å, Structure of 10 in complex with GDP-KRAS
9IAW 1.0 Å, Structure of 5 in complex with GDP-KRAS
12XE 1.01 Å, Crystal structure of KRAS(Q61K) bound to GppNHp and ligand
8ONV 1.01 Å, KRAS-G13D in complex with BI-2493
6P0Z 1.01 Å, Crystal structure of N-acetylated KRAS (2-169) bound to GDP and Mg
9IB5 1.01 Å, Structure of 18 (BI-2493) in complex with GDP-KRAS
8AZZ 1.02 Å, KRAS-G12V in complex with BI-2865
8AZX 1.04 Å, KRAS-G12C in complex with BI-2865
8B00 1.04 Å, KRAS-G13D in complex with BI-2865
8TVK 1.04 Å, KRAS 1-169 G12C Mutant at 100k
4QL3 1.04 Å, Crystal Structure of a GDP-bound G12R Oncogenic Mutant of Human GTPase KRas
8AZV 1.05 Å, KRAS in complex with BI-2865

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