8QFB: Human MPP8 C-terminal region

Crystal structure of human MPP8 C-terminal region (residues 565-860). Determined by X-ray diffraction at 3.04 Å resolution. Released 11 Sept 2024.

Method: X-ray diffraction
Resolution: 3.04 Å
Organism: Homo sapiens
Chains: 8
Atoms: 17,740
Mol. weight: 295.36 kDa
Released: 11 Sept 2024

Explore 8QFB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QFB contains 97 α-helices and 104 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.

Chain A: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	564-566	3
α-helix	567-576	10
α-helix	579-587	9
α-helix	604-610	7
α-helix	614-621	8
α-helix	637-643	7
α-helix	647-655	9
α-helix	670-677	8
α-helix	680-688	9
β-strand	696	1	4
β-strand	702	1	4
α-helix	703-709	7
α-helix	713-737	25
β-strand	742-747	6	5
β-strand	752-755	4	5
α-helix	756-758	3
β-strand	761-768	8	6
β-strand	778-789	12	5
β-strand	794-797	4	5
β-strand	804-809	6	6
β-strand	812-814	3	6
β-strand	816	1	5
β-strand	824-826	3	5
α-helix	829-830	2
β-strand	832-840	9	6
β-strand	849-859	11	5

Chain B: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	569-575	7
α-helix	579-587	9
α-helix	604-610	7
α-helix	614-621	8
α-helix	637-643	7
α-helix	647-655	9
α-helix	670-677	8
α-helix	680-688	9
β-strand	696	1	1
β-strand	702	1	1
α-helix	703-709	7
α-helix	713-738	26
β-strand	742-747	6	2
β-strand	752-755	4	2
α-helix	756-758	3
β-strand	761-768	8	3
β-strand	778-790	13	2
β-strand	793-797	5	2
β-strand	804-809	6	3
β-strand	812-814	3	3
β-strand	816	1	2
β-strand	824-826	3	2
α-helix	829-830	2
β-strand	832-840	9	3
β-strand	849-859	11	2

Chain C: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	569-575	7
α-helix	579-587	9
α-helix	604-610	7
α-helix	614-621	8
α-helix	637-643	7
α-helix	647-655	9
α-helix	670-676	7
α-helix	680-688	9
β-strand	696	1	7
β-strand	702	1	7
α-helix	703-709	7
α-helix	713-737	25
β-strand	743-747	5	8
β-strand	752-755	4	8
α-helix	756-758	3
β-strand	761-768	8	9
β-strand	778-790	13	8
β-strand	793-797	5	8
β-strand	804-809	6	9
β-strand	812-813	2	9
β-strand	816	1	8
β-strand	824-826	3	8
α-helix	829-830	2
β-strand	832-840	9	9
β-strand	849-858	10	8

Chain D: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	567-576	10
α-helix	579-587	9
α-helix	604-610	7
α-helix	614-621	8
α-helix	637-643	7
α-helix	647-655	9
α-helix	670-677	8
α-helix	680-688	9
β-strand	696	1	10
β-strand	702	1	10
α-helix	703-709	7
α-helix	713-737	25
β-strand	743-747	5	11
β-strand	752-755	4	11
α-helix	756-758	3
β-strand	761-768	8	12
β-strand	778-790	13	11
β-strand	793-797	5	11
β-strand	804-809	6	12
β-strand	812-813	2	12
β-strand	816	1	11
β-strand	824-826	3	11
α-helix	829-830	2
β-strand	832-840	9	12
β-strand	849-858	10	11

Chains E and G: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	568-576	9
α-helix	579-587	9
α-helix	604-610	7
α-helix	614-621	8
α-helix	637-643	7
α-helix	647-655	9
α-helix	670-677	8
α-helix	680-688	9
β-strand	696	1	13
β-strand	702	1	13
α-helix	703-709	7
α-helix	713-737	25
β-strand	743-747	5	14
β-strand	752-755	4	14
α-helix	756-758	3
β-strand	761-768	8	15
β-strand	778-790	13	14
β-strand	793-797	5	14
β-strand	804-809	6	15
β-strand	812-813	2	15
β-strand	816	1	14
β-strand	824-826	3	14
α-helix	829-830	2
β-strand	832-840	9	15
β-strand	849-858	10	14

Chain F: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	568-575	8
α-helix	579-587	9
α-helix	604-610	7
α-helix	614-621	8
α-helix	637-643	7
α-helix	647-655	9
α-helix	670-677	8
α-helix	680-688	9
β-strand	696	1	16
β-strand	702	1	16
α-helix	703-709	7
α-helix	713-737	25
β-strand	743-747	5	17
β-strand	752-755	4	17
α-helix	756-758	3
β-strand	761-768	8	18
β-strand	778-790	13	17
β-strand	793-797	5	17
β-strand	804-809	6	18
β-strand	812-814	3	18
β-strand	816	1	17
β-strand	824-826	3	17
α-helix	829-830	2
β-strand	832-840	9	18
β-strand	849-858	10	17

Chain H: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	568-576	9
α-helix	579-587	9
α-helix	604-610	7
α-helix	614-621	8
α-helix	637-643	7
α-helix	647-655	9
α-helix	670-677	8
α-helix	680-688	9
β-strand	696	1	22
β-strand	702	1	22
α-helix	703-709	7
α-helix	713-737	25
β-strand	742-747	6	23
β-strand	752-755	4	23
α-helix	756-758	3
β-strand	761-768	8	24
β-strand	778-790	13	23
β-strand	793-797	5	23
β-strand	804-809	6	24
β-strand	812-814	3	24
β-strand	816	1	23
β-strand	824-826	3	23
α-helix	829-830	2
β-strand	832-840	9	24
β-strand	849-859	11	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
M-phase phosphoprotein 8	A, B, C, D, E, F, G, H	protein	336	Homo sapiens	Q99549 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>8QFB_1 M-phase phosphoprotein 8 (chains A, B, C, D, E, F, G, H)
MGSSHHHHHHSSGLVPRGSHMEDFQKHLDGKDENFAATDAIPSNVLRDAVKNGDYITVKV
ALNSNEEYNLDQEDSSGMTLVMLAAAGGQDDLLRLLITKGAKVNGRQKNGTTALIHAAEK
NFLTTVAILLEAGAFVNVQQSNGETALMKACKRGNSDIVRLVIECGADCNILSKHQNSAL
HFAKQSNNVLVYDLLKNHLETLSRVAEETIKDYFEARLALLEPVFPIACHRLCEGPDFST
DFNYKPPQNIPEGSGILLFIFHANFLGKEVIARLCGPCSVQAVVLNDKFQLPVFLDSHFV
YSFSPVAGPNKLFIRLTEAPSAKVKLLIGAYRVQLQ

Primary citation

Structure and Methyl-lysine Binding Selectivity of the HUSH Complex Subunit MPP8. Nikolopoulos, N., Oda, S.I., Prigozhin, D.M. et al. J Mol Biol (2024) 437:168890-168890. DOI 10.1016/j.jmb.2024.168890 · 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
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
3SVM 2.31 Å, Human MPP8 - human DNMT3AK47me2 peptide
3QO2 2.49 Å, Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9

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