3R93: Chromo domain of M-phase phosphoprotein 8

Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide. Determined by X-ray diffraction at 2.06 Å resolution. Released 6 Apr 2011.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 8
Atoms: 2,272
Mol. weight: 35.81 kDa
Released: 6 Apr 2011

Explore 3R93 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3R93 contains 15 α-helices and 22 β-strands across 8 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, C and D: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	58-60	3	1
β-strand	61-70	10	2
β-strand	73-80	8	2
α-helix	85-87	3
β-strand	89-92	4	2
α-helix	93-96	4
α-helix	100-113	14

Chain B: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	58-60	3	3
β-strand	61-70	10	4
β-strand	73-80	8	4
α-helix	85-87	3
β-strand	89-92	4	4
α-helix	93-95	3
α-helix	100-112	13

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
α-helix	9-10	2
β-strand	13-14	2	7

Chains F and G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-8	3	3
α-helix	9-10	2

Chain H: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	6
β-strand	13-14	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
M-phase phosphoprotein 8	A, B, C, D	protein	62	Homo sapiens	Q99549 (AlphaFold model)
H3K9Me3 peptide	E, F, G, H	protein	15		Q71DI3 (AlphaFold model)

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

>3R93_1 M-phase phosphoprotein 8 (chains A, B, C, D)
GEDVFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEFRKKIAENK
AK

Sequence of entity 2 (E, F, G, H), FASTA

>3R93_2 H3K9Me3 peptide (chains E, F, G, H)
ARTKQTARKSTGGKA

Primary citation

Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9. Li, J., Li, Z., Ruan, J. et al. PLoS One (2011) 6:e25104-e25104. DOI 10.1371/journal.pone.0025104 · PubMed

Other PDB entries of the same protein (UniProt Q99549 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6V2S 1.6 Å, Crystal Structure of chromodomain of MPP8 in complex with inhibitor UNC3866
9H77 2.01 Å, MPP8 chromodomain in complex with nanobody 3A02
7M5U 2.02 Å, Crystal structure of human MPP8 chromodomain in complex with peptidomimetic ligand UNC5246
3LWE 2.05 Å, The crystal structure of MPP8
3SVM 2.31 Å, Human MPP8 - human DNMT3AK47me2 peptide
3QO2 2.49 Å, Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9
8QFB 3.04 Å, Crystal structure of human MPP8 C-terminal region (residues 565-860)

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