8TBG: Tricomplex of RMC-7977, HRAS WT, and CypA

Tricomplex of RMC-7977, HRAS WT, and CypA. Determined by X-ray diffraction at 1.2 Å resolution. Released 7 Feb 2024.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,398
Mol. weight: 77.03 kDa
Ligands: GNP, MG, ZNI
Released: 7 Feb 2024

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

Secondary structure: helices and β-sheets

8TBG contains 24 α-helices and 39 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	1	1
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	62-68	7
α-helix	69-74	6
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	152-164	13

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	2
α-helix	16-25	10
β-strand	37-46	10	2
β-strand	49-58	10	2
α-helix	62-68	7
α-helix	69-74	6
β-strand	77-83	7	2
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	2
α-helix	127-137	11
β-strand	141-143	3	2
β-strand	145	1	3
β-strand	150	1	3
α-helix	152-164	13

Chain C: 5 helices, 12 β-strands

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

Chain D: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	7
β-strand	15-24	10	7
α-helix	30-41	12
β-strand	52	1	7
β-strand	55-57	3	7
β-strand	61-64	4	7
β-strand	77-78	2	8
β-strand	80	1	8
β-strand	83	1	9
β-strand	97-100	4	7
β-strand	108	1	9
β-strand	112-115	4	7
α-helix	120-122	3
β-strand	128-134	7	7
α-helix	136-142	7
α-helix	143-145	3
β-strand	156-164	9	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTPase HRas	A, B	protein	167	Homo sapiens	P01112 (AlphaFold model)
Peptidyl-prolyl cis-trans isomerase A	C, D	protein	166	Homo sapiens	P62937 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8TBG_1 GTPase HRas (chains A, B)
GMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTA
GQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCD
LAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

Sequence of entity 2 (C, D), FASTA

>8TBG_2 Peptidyl-prolyl cis-trans isomerase A (chains C, D)
SMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPG
FMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT
EWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2
MG	Magnesium ion	Mg	2
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

Water and common crystallization additives (GOL) are not listed.

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 P01112 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2CE2 1.0 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GDP
2EVW 1.05 Å, Crystal structure analysis of a fluorescent form of H-Ras p21 in complex with R-caged GTP
24SQ 1.08 Å, Human HRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AP6296
2CLD 1.22 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GDP (2)
2CL6 1.24 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with S-caged GTP
2CL7 1.25 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GTP
5WDQ 1.25 Å, H-Ras mutant L120A bound to GMP-PNP at 100K
1CTQ 1.26 Å, Structure of P21RAS in complex with gppnhp at 100 K
2CLC 1.3 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GTP (2)
3K8Y 1.3 Å, Allosteric modulation of H-Ras GTPase
3OIW 1.3 Å, H-RasG12V with allosteric switch in the "on" state
3TGP 1.31 Å, Room temperature H-ras

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