9C4S: Menin mutant G331R

Menin mutant G331R in complex with MLL peptide. Determined by X-ray diffraction at 1.54 Å resolution. Released 21 May 2025.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,283
Mol. weight: 56.81 kDa
Ligands: PG0
Released: 21 May 2025

Explore 9C4S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C4S contains 33 α-helices and 14 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: 33 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	11	1
β-strand	13	1	1
α-helix	16-28	13
α-helix	34-45	12
α-helix	46-50	5
β-strand	81	1	1
α-helix	83-100	18
α-helix	103-105	3
α-helix	109-111	3
α-helix	115-128	14
β-strand	137	1	2
α-helix	143-149	7
α-helix	154-167	14
β-strand	174-177	4	3
β-strand	182-186	5	3
α-helix	188-190	3
β-strand	192-194	3	3
α-helix	203-205	3
α-helix	212-216	5
β-strand	219	1	4
α-helix	220-225	6
β-strand	228-229	2	3
α-helix	232-241	10
β-strand	246	1	5
β-strand	252	1	5
α-helix	254-269	16
α-helix	277-289	13
α-helix	291-292	2
α-helix	296-297	2
α-helix	298-312	15
α-helix	319-330	12
α-helix	334-348	15
β-strand	352	1	4
α-helix	358-366	9
α-helix	367-371	5
α-helix	372-384	13
α-helix	403-405	3
α-helix	407-424	18
α-helix	434-445	12
α-helix	449-452	4
β-strand	456-457	2	6
β-strand	550-551	2	6
α-helix	556-561	6
α-helix	562-565	4
α-helix	572-579	8

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Menin	A	protein	489	Homo sapiens	O00255 (AlphaFold model)
MLL cleavage product N320	B	protein	14	Homo sapiens	Q03164

Sequence of entity 1 (A), FASTA

>9C4S_1 Menin (chains A)
GGSSSMGLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVGL
TYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFK
DRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAE
VTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLE
LLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRD
EHIYPYMYLARYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNL
LKEAASLLEAGSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRF
EGQVRQKVRIVSVPAPAASPPPEGPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQ
VQMKKQKVS

Sequence of entity 2 (B), FASTA

>9C4S_2 MLL cleavage product N320 (chains B)
XSARWRFPARPGTX

Ligands and cofactors

ID	Name	Formula	Copies
PG0	2-(2-methoxyethoxy)ethanol	C5 H12 O3	1

Water and common crystallization additives (SO4, 1PE, EDO) are not listed.

Primary citation

Drug-resistant menin variants retain high binding affinity and interactions with MLL1. Ray, J., Clegg, B., Grembecka, J. et al. J Biol Chem (2024) 300:107777-107777. DOI 10.1016/j.jbc.2024.107777 · PubMed

Other PDB entries of the same protein (UniProt O00255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O5I 1.24 Å, Menin in complex with MI-3454
4GQ4 1.27 Å, Human menin with bound inhibitor MI-2-2
8VA5 1.3 Å, Menin mutant - T349M in complex with Ziftomenib (KO-539)
9C4Y 1.31 Å, Menin mutant - T349M
9C4W 1.4 Å, Menin mutant - G331R
9C4Z 1.4 Å, Menin mutant - G331D
4OG4 1.45 Å, Human menin with bound inhibitor MIV-3S
4GPQ 1.46 Å, Structural insights into inhibition of the bivalent menin-MLL interaction by small…
9C4T 1.46 Å, menin mutant M327I in complex with MLL peptide
9C4V 1.47 Å, Menin mutant G331D in complex with MLL peptide
4OG6 1.49 Å, Human menin with bound inhibitor MIV-4
5DB0 1.5 Å, Menin in complex with MI-352

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