9F99: MUS81-EME1 bound by compound 10

Crystal structure of MUS81-EME1 bound by compound 10. Determined by X-ray diffraction at 2.8 Å resolution. Released 19 Jun 2024.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,145
Mol. weight: 282.48 kDa
Ligands: A1IA5, MG
Released: 19 Jun 2024

Explore 9F99 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F99 contains 63 α-helices and 74 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: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	1
β-strand	267-274	8	2
α-helix	275-277	3
α-helix	286-293	8
β-strand	298-301	4	2
β-strand	308-314	7	2
β-strand	325-336	12	2
α-helix	337-345	9
α-helix	348-357	10
β-strand	363-369	7	2
α-helix	381-393	13
α-helix	397	1
β-strand	398-402	5	2
α-helix	405-422	18
β-strand	428-430	3	1
β-strand	452-453	2	1
β-strand	455	1	2
α-helix	456-459	4

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	253-256	4	3
α-helix	258-262	5
α-helix	266-275	10
β-strand	279-282	4	3
β-strand	290-294	5	3
β-strand	308	1	3
β-strand	311-317	7	3
α-helix	318-326	9
α-helix	343-354	12
β-strand	358-364	7	3
α-helix	405-418	14
β-strand	422-426	5	3
α-helix	429-445	17

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	4
β-strand	267-274	8	5
α-helix	275-278	4
α-helix	286-293	8
β-strand	298-301	4	5
β-strand	308-314	7	5
β-strand	325-336	12	5
α-helix	337-345	9
α-helix	349-357	9
β-strand	363-369	7	5
α-helix	381-390	10
α-helix	391-395	5
β-strand	398-402	5	5
α-helix	405-422	18
β-strand	428-430	3	4
α-helix	448	1
α-helix	450	1
β-strand	452-453	2	4
β-strand	454-455	2	5
α-helix	456-459	4

Chain D: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	253-256	4	6
α-helix	258-261	4
α-helix	266-275	10
β-strand	279-281	3	6
β-strand	290-294	5	6
β-strand	308-310	3	6
β-strand	311-312	2	7
β-strand	313-314	2	6
β-strand	315-317	3	8
α-helix	318-326	9
α-helix	343-353	11
β-strand	358-359	2	7
β-strand	360	1	9
β-strand	362-364	3	8
α-helix	405-418	14
β-strand	422	1	9
β-strand	425-426	2	8
α-helix	429-443	15

Chain E: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	10
β-strand	267-274	8	11
α-helix	275-277	3
α-helix	286-293	8
β-strand	298-301	4	11
β-strand	308-314	7	11
β-strand	325-336	12	11
α-helix	337-345	9
α-helix	349-357	9
β-strand	363-369	7	11
α-helix	381-393	13
β-strand	398-399	2	11
β-strand	402	1	11
α-helix	405-422	18
α-helix	426-427	2
β-strand	428-430	3	10
α-helix	448	1
α-helix	450	1
β-strand	452-453	2	10
β-strand	454	1	11
α-helix	455	1
α-helix	456-459	4

Chain F: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	253-256	4	12
α-helix	258-262	5
α-helix	266-275	10
β-strand	279-281	3	12
β-strand	290-294	5	12
β-strand	308	1	12
β-strand	311-317	7	12
α-helix	318-326	9
α-helix	343-354	12
β-strand	358-364	7	12
α-helix	405-418	14
β-strand	421-426	6	12
α-helix	429-443	15

Chain G: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	13
β-strand	268-274	7	13
α-helix	275-278	4
α-helix	286-293	8
β-strand	298-301	4	13
β-strand	308-313	6	13
β-strand	325-336	12	13
α-helix	337-345	9
α-helix	349-357	9
β-strand	363-369	7	13
α-helix	381-390	10
α-helix	391-395	5
β-strand	398-401	4	13
α-helix	405-422	18
β-strand	428-431	4	13
α-helix	448	1
α-helix	450	1
β-strand	452-455	4	13
α-helix	456-459	4

Chain H: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	253-256	4	14
α-helix	260-262	3
α-helix	266-275	10
β-strand	279-282	4	14
β-strand	290-294	5	14
β-strand	308	1	14
β-strand	311-314	4	14
β-strand	317	1	14
α-helix	318-327	10
α-helix	343-354	12
β-strand	358-364	7	14
α-helix	405-418	14
β-strand	422-426	5	14
α-helix	429-444	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Crossover junction endonuclease MUS81	A, C, E, G	protein	308	Homo sapiens	Q96NY9 (AlphaFold model)
Crossover junction endonuclease EME1	B, D, F, H	protein	326	Homo sapiens	Q96AY2 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>9F99_1 Crossover junction endonuclease MUS81 (chains A, C, E, G)
GSSAELASEAGVQQQPLELRPGEYRVLLCVDIGETRGGGHRPELLRELQRLHVTHTVRKL
HVGDFVWVAQETNPRDPANPGELVLDHIVERKRLDDLCSSIIDGRFREQKFRLKRCGLER
RVYLVEEHGSVHNLSLPESTLLQAVTNTQVIDGFFVKRTADIKESAAYLALLTRGLQRLY
QGHTLRSRPWGTPGNPESGAMTSPNPLCSLLTFSDFNAGAIKNKAQSVREVFARQLMQVR
GVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTLSQL
YCSYGPLT

Sequence of entity 2 (B, D, F, H), FASTA

>9F99_2 Crossover junction endonuclease EME1 (chains B, D, F, H)
GEECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSEDRE
DWVEEPTVLVLLRAEAFVSMIDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIV
DQEKCFSAQNPPRRGKQGANKQTKKQQQRQPEASIGSMVSRVDAEEALVDLQLHTEAQAQ
IVQSWKELADFTCAFTKAVAEAPFKKLRDETTFSFCLESDWAGGVKVDLAGRGLALVWRR
QIQQLNRVSLEMASAVVNAYPSPQLLVQAYQQCFSDKERQNLLADIQVRRGEGVTSTSRR
IGPELSRRIYLQMTTLQPHLSLDSAD

Ligands and cofactors

ID	Name	Formula	Copies
A1IA5	2-(4-chlorophenyl)-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid	C11 H7 Cl N2 O4	4
MG	Magnesium ion	Mg	8

Primary citation

Fragment-Based Discovery of Novel MUS81 Inhibitors. Collie, G.W., Borjesson, U., Chen, Y. et al. ACS Med Chem Lett (2024) 15:1151-1158. DOI 10.1021/acsmedchemlett.3c00453 · PubMed

Other PDB entries of the same protein (UniProt Q96NY9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BU5 1.8 Å, Crystal Structure of Human SLX4 and MUS81
9F9L 2.02 Å, Crystal structure of MUS81-EME1 bound by compound 16.
9F98 2.15 Å, Crystal structure of MUS81-EME1, apo form.
9F9M 2.47 Å, Crystal structure of MUS81-EME1 bound by compound 21.
9F9K 2.73 Å, Crystal structure of MUS81-EME1 bound by compound 15.
4P0P 2.8 Å, Crystal structure of Human Mus81-Eme1 in complex with 5'-flap DNA, and Mg2+
4P0Q 2.85 Å, Crystal structure of Human Mus81-Eme1 in complex with 5'-flap DNA
9F9A 2.91 Å, Crystal structure of MUS81-EME1 bound by compound 12.
7F6L 3.2 Å, Crystal structure of human MUS81-EME2 complex
2ZIX 3.5 Å, Crystal structure of the Mus81-Eme1 complex
4P0S 6.0 Å, human Mus81-Eme1-3'flap DNA complex
4P0R 6.5 Å, human Mus81-Eme1-3'flap DNA complex

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