8TBI: Tricomplex of RMC-7977, NRAS WT, and CypA

Tricomplex of RMC-7977, NRAS WT, and CypA. Determined by X-ray diffraction at 1.59 Å resolution. Released 7 Feb 2024.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,201
Mol. weight: 78.39 kDa
Ligands: ZNI, MG, GNP
Released: 7 Feb 2024

Explore 8TBI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TBI contains 22 α-helices and 36 β-strands across 4 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
α-helix	1	1
β-strand	2-9	8	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	62-68	7
α-helix	69-74	6
β-strand	77-83	7	1
α-helix	87-104	18
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
α-helix	152-166	15

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	2
α-helix	16-25	10
β-strand	37-46	10	2
β-strand	49-58	10	2
α-helix	62-67	6
α-helix	69-74	6
β-strand	77-83	7	2
α-helix	87-104	18
β-strand	111-116	6	2
α-helix	127-137	11
β-strand	141-143	3	2
α-helix	152-168	17

Chain C: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	3
β-strand	15-24	10	3
α-helix	30-41	12
β-strand	52-57	6	3
β-strand	61-64	4	3
β-strand	77-78	2	4
β-strand	80	1	4
β-strand	83	1	5
β-strand	97-100	4	3
β-strand	108	1	5
β-strand	112-115	4	3
α-helix	120-122	3
β-strand	128-132	5	3
α-helix	136-142	7
α-helix	143-145	3
β-strand	156-163	8	3

Chain D: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-12	8	6
β-strand	15-24	10	6
α-helix	30-41	12
β-strand	52-57	6	6
β-strand	61-64	4	6
β-strand	77-78	2	7
β-strand	80	1	7
β-strand	83	1	8
β-strand	97-100	4	6
β-strand	108	1	8
β-strand	112-115	4	6
α-helix	120-122	3
β-strand	128-132	5	6
α-helix	136-142	7
α-helix	143-145	3
β-strand	156-163	8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTPase NRas	A, B	protein	173	Homo sapiens	P01111 (AlphaFold model)
Peptidyl-prolyl cis-trans isomerase A	C, D	protein	166	Homo sapiens	P62937 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8TBI_1 GTPase NRas (chains A, B)
SMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTA
GQEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCD
LPTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLN

Sequence of entity 2 (C, D), FASTA

>8TBI_2 Peptidyl-prolyl cis-trans isomerase A (chains C, D)
SMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPG
FMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT
EWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

Ligands and cofactors

ID	Name	Formula	Copies
ZNI	(1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-…	C47 H60 N8 O6 S	2
MG	Magnesium ion	Mg	2
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

Primary citation

Concurrent inhibition of oncogenic and wild-type RAS-GTP for cancer therapy. Holderfield, M., Lee, B.J., Jiang, J. et al. Nature (2024) 629:919-926. DOI 10.1038/s41586-024-07205-6 · PubMed

Other PDB entries of the same protein (UniProt P01111 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BG8 1.2 Å, Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61R, and CypA
24SR 1.23 Å, Human NRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AP6296
7F68 1.24 Å, Crystal structure of N-ras S89D
9BG3 1.33 Å, Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61K, and CypA
6ZIO 1.55 Å, Crystal structure of NRAS (C118S) in complex with GDP
9Y3W 1.56 Å, Crystal structure of NRas-G12D in complex with GDP and compound 13
9BG0 1.64 Å, Tri-complex of Daraxonrasib (RMC-6236), NRAS WT, and CypA
3CON 1.65 Å, Crystal structure of the human NRAS GTPase bound with GDP
6WGH 1.65 Å, Crystal structure of GDP-bound NRAS with ten residues long internal tandem duplication…
5UHV 1.67 Å, wild-type NRas bound to GppNHp
9Y1Y 1.7 Å, Crystal structure of NRas-G12D in complex with GDP and compound 7
9Y1X 1.72 Å, Crystal structure of NRas-G12D in complex with GDP and IACS-56676

Browse structure collections

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