3U88: Human menin

Name: PDB 3U88: Crystal structure of human menin in complex with MLL1 and LEDGF
Published: 2012-02-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of human menin in complex with MLL1 and LEDGF. Determined by X-ray diffraction at 3.0 Å resolution. Released 15 Feb 2012.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,881
Mol. weight: 161.94 kDa
Ligands: CHD, GGB, 0BR, GLV
Released: 15 Feb 2012

Explore 3U88 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3U88 contains 75 α-helices and 34 β-strands across 6 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: 29 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
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	53-54	2	2
β-strand	63-67	5	3
α-helix	68-69	2
β-strand	75-79	5	3
β-strand	81	1	1
α-helix	83-98	16
α-helix	115-126	12
α-helix	143-148	6
α-helix	154-167	14
β-strand	174-177	4	4
β-strand	182-186	5	4
α-helix	188-190	3
β-strand	192-194	3	4
β-strand	198	1	5
β-strand	205	1	5
α-helix	212-217	6
α-helix	223-225	3
β-strand	228-229	2	4
α-helix	232-241	10
β-strand	246	1	6
β-strand	251-253	3	6
α-helix	254-269	16
α-helix	277-289	13
α-helix	298-312	15
α-helix	319-330	12
α-helix	334-348	15
α-helix	355-357	3
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	456-458	3	7
β-strand	550-552	3	7
α-helix	556-560	5
α-helix	572-579	8

Chain B: 29 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
β-strand	13	1	8
α-helix	16-28	13
α-helix	34-45	12
α-helix	46-50	5
β-strand	53-54	2	9
β-strand	63-66	4	10
β-strand	76-79	4	10
β-strand	81	1	8
α-helix	83-98	16
α-helix	103-105	3
α-helix	115-126	12
α-helix	143-148	6
α-helix	154-167	14
β-strand	174-177	4	11
β-strand	182-186	5	11
α-helix	188-190	3
β-strand	192-194	3	11
α-helix	212-216	5
α-helix	220-225	6
β-strand	228-229	2	11
α-helix	232-241	10
β-strand	246-248	3	12
β-strand	251-253	3	12
α-helix	254-269	16
α-helix	277-289	13
α-helix	291-292	2
α-helix	298-312	15
α-helix	319-330	12
α-helix	334-348	15
α-helix	355-357	3
α-helix	358-366	9
α-helix	367-371	5
α-helix	372-384	13
α-helix	402-405	4
α-helix	407-424	18
α-helix	434-444	11
α-helix	449-452	4
β-strand	456-458	3	13
β-strand	550-552	3	13
α-helix	556-559	4
α-helix	572-578	7

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	349-362	14
β-strand	363	1	14
β-strand	368	1	14
α-helix	370-380	11
α-helix	387-391	5
α-helix	394-403	10
α-helix	410-427	18

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	354-361	8
α-helix	371-381	11
α-helix	387-390	4
α-helix	394-403	10
α-helix	411-429	19

Chain M: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	24-28	5
β-strand	33-35	3	6
α-helix	39	1
β-strand	107-108	2	2
α-helix	114-133	20

Chain N: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
α-helix	31-32	2
β-strand	33-35	3	12
α-helix	39	1
β-strand	107-108	2	9
α-helix	114-132	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Menin	A, B	protein	550	Homo sapiens	O00255 (AlphaFold model)
Histone-lysine N-methyltransferase 2A	M, N	protein	75	Homo sapiens	Q03164
Lens epithelium-derived growth factor	C, D	protein	89	Homo sapiens	O75475 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3U88_1 Menin (chains A, B)
SGLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVIPTNVPE
LTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKK
VSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSED
HAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMV
CAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLT
LYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEI
YKEFFEVANDVIPNLLKEAASLLEAGEERPGEQSQGTQSQGSALQDPECFAHLLRFYDGI
CKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSGTVAGTARGPEGGSTAQVPAP
TASPPPEGPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQVQMKKQKVSTPSDYTL
SFLKRQRKGL

Sequence of entity 2 (M, N), FASTA

>3U88_2 Histone-lysine N-methyltransferase 2A (chains M, N)
SRWRFPARPGTGRRGLGGAPRQRVPALLRVGPGFDAALQVSAAIGTNLRRFRAVFGESGG
GGGSGEDEQFLGFGS

Sequence of entity 3 (C, D), FASTA

>3U88_3 Lens epithelium-derived growth factor (chains C, D)
SMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRF
KVSQVIMEKSTMLYNKFKNMFLVGEGDSV

Ligands and cofactors

ID	Name	Formula	Copies
CHD	Cholic acid	C24 H40 O5	2
GGB	L-canavanine	C5 H12 N4 O3	5
0BR	(4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol	C20 H26 N2 O2	2
GLV	Glyoxylic acid	C2 H2 O3	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

The same pocket in menin binds both MLL and JUND but has opposite effects on transcription. Huang, J., Gurung, B., Wan, B. et al. Nature (2012) 482:542-546. DOI 10.1038/nature10806 · 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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