7U5V: Histone-lysine N-methyltransferase 2A

Crystal structure of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and Borealin peptide. Determined by X-ray diffraction at 2.59 Å resolution. Released 27 Sept 2023.

Method: X-ray diffraction
Resolution: 2.59 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,027
Mol. weight: 19.54 kDa
Ligands: SAH, ZN
Released: 27 Sept 2023

Explore 7U5V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7U5V contains 7 α-helices and 13 β-strands across 1 chain. 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3824-3830	7
β-strand	3831-3835	5	1
β-strand	3841-3845	5	1
β-strand	3849	1	2
β-strand	3854-3857	4	3
β-strand	3861-3864	4	4
α-helix	3865-3867	3
α-helix	3868-3877	10
α-helix	3880-3882	3
β-strand	3884-3886	3	4
β-strand	3891-3894	4	4
α-helix	3901-3904	4
α-helix	3905	1
β-strand	3906-3907	2	5
β-strand	3913-3920	8	3
β-strand	3923-3930	8	3
β-strand	3934	1	2
α-helix	3938	1
β-strand	3939-3940	2	1
β-strand	3941-3942	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase 2A	A	protein	159	Homo sapiens	Q03164
Borealin	C	protein	9	Homo sapiens	Q53HL2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7U5V_1 Histone-lysine N-methyltransferase 2A (chains A)
SMDLPMPMRFRALAAASAAAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDK
REKYYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFA
MRKIYRGEELTYDYAFPIEDASNKLPCNCGAKKCRKFLN

Sequence of entity 2 (C), FASTA

>7U5V_2 Borealin (chains C)
LQTARVKRC

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
ZN	Zinc ion	Zn	1

Primary citation

Non-canonical MLL1 activity regulates centromeric phase separation and genome stability. Sha, L., Yang, Z., An, S. et al. Nat Cell Biol (2023) 25:1637-1649. DOI 10.1038/s41556-023-01270-1 · PubMed

Other PDB entries of the same protein (UniProt Q03164), best resolution first:

3EMH 1.37 Å, Structural basis of WDR5-MLL interaction
9C4T 1.46 Å, menin mutant M327I in complex with MLL peptide
9C4V 1.47 Å, Menin mutant G331D in complex with MLL peptide
7S79 1.53 Å, Structure of HLA-B*07:02 in complex with synthetic phosphono-mll peptide analog
9C4S 1.54 Å, Menin mutant G331R in complex with MLL peptide
4GQ6 1.55 Å, Human menin in complex with MLL peptide
7S7D 1.56 Å, Structure of HLA-B*07:02 in complex with synthetic sulfo-mll peptide analog
9C4U 1.57 Å, Menin mutant T349M in complex with MLL peptide
7S8E 1.6 Å, Structure of HLA-B*07:02 in complex with MLL(747-755) phosphopeptide and bound glycerol
4ESG 1.7 Å, X-ray structure of WDR5-MLL1 Win motif peptide binary complex
3EG6 1.72 Å, Structure of WDR5 bound to MLL1 peptide
3LQH 1.72 Å, Crystal structure of MLL1 PHD3-Bromo in the free form

Browse structure collections

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