9C1B: GDP-bound human M-RAS protein in crystal form II

Crystal structure of GDP-bound human M-RAS protein in crystal form II. Determined by X-ray diffraction at 2.27 Å resolution. Released 11 Sept 2024.

Method: X-ray diffraction
Resolution: 2.27 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,932
Mol. weight: 103.96 kDa
Ligands: GDP, MG
Released: 11 Sept 2024

Explore 9C1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C1B contains 31 α-helices and 32 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.

Chains A, B and D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	1
α-helix	26-34	9
β-strand	48-56	9	1
β-strand	59-67	9	1
α-helix	76-84	9
β-strand	87-93	7	1
α-helix	97-101	5
α-helix	103-114	12
β-strand	121-126	6	1
α-helix	131-133	3
α-helix	138-148	11
β-strand	152-154	3	1
β-strand	156	1	2
α-helix	161	1
β-strand	162	1	2
α-helix	164-176	13

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	5
α-helix	26-34	9
β-strand	48-56	9	5
β-strand	59-67	9	5
α-helix	76-84	9
β-strand	87-93	7	5
α-helix	97-101	5
α-helix	103-114	12
β-strand	121-126	6	5
α-helix	131-133	3
α-helix	138-148	11
β-strand	152-154	3	5
β-strand	156	1	6
β-strand	162	1	6
α-helix	164-176	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein M-Ras	A, B, C, D	protein	219	Homo sapiens	O14807 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9C1B_1 Ras-related protein M-Ras (chains A, B, C, D)
MGHHHHHHENLYFQGMATSAVPSDNLPTYKLVVVGDGGVGKSALTIQFFQKIFVPDYDPT
IEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDR
FHQLILRVKDRESFPMILVANKVDLMHLRKITREQGKEMATKHNIPYIETSAKDPPLNVD
KAFHDLVRVIRQQIPEKSQKKKKKTKWRGDRATGTHKLQ

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	4
MG	Magnesium ion	Mg	4

Water and common crystallization additives (PGE, PEG, PG4) are not listed.

Primary citation

Crystal structure of the GDP-bound human M-RAS protein in two crystal forms. Bester, S.M., Abrahamsen, R., Rodrigues Samora, L. et al. Acta Crystallogr F Struct Biol Commun (2024) 80:220-227. DOI 10.1107/S2053230X24007969 · PubMed

Other PDB entries of the same protein (UniProt O14807 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9O0P 1.5 Å, Crystal structure of GDP-bound mutant MRAS in complex with MRTX1133
9O0Q 1.9 Å, Crystal structure of GMPPNP-bound mutant MRAS in complex with MRTX1133
7TXH 1.95 Å, Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca
9C1A 1.96 Å, Crystal structure of GDP-bound human M-RAS protein in crystal form I
9B4R 2.1 Å, Crystal structure of MRAS bound to GMPPNP
7TVF 2.17 Å, Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom
9B4T 2.75 Å, Crystal structure of the MRAS-p110alpha complex
9MEZ 2.8 Å, Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain)
7UPI 2.89 Å, Cryo-EM structure of SHOC2-PP1c-MRAS holophosphatase complex
7SD0 2.95 Å, Cryo-EM structure of the SHOC2:PP1C:MRAS complex

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