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- PDB-9f9l: Crystal structure of MUS81-EME1 bound by compound 16. -

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Basic information

Entry
Database: PDB / ID: 9f9l
TitleCrystal structure of MUS81-EME1 bound by compound 16.
Components(Crossover junction endonuclease ...) x 2
KeywordsHYDROLASE / Endonuclease / fragment / drug discovery
Function / homology
Function and homology information


3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / endodeoxyribonuclease complex / osteoblast proliferation / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / double-strand break repair via break-induced replication / DNA catabolic process ...3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / endodeoxyribonuclease complex / osteoblast proliferation / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / double-strand break repair via break-induced replication / DNA catabolic process / mitotic intra-S DNA damage checkpoint signaling / Resolution of D-loop Structures through Holliday Junction Intermediates / replication fork processing / nuclear replication fork / heterochromatin / replication fork / Fanconi Anemia Pathway / double-strand break repair / endonuclease activity / DNA repair / nucleolus / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Crossover junction endonuclease Mus81 / EME1/EME2, C-terminal domain / : / : / Crossover junction endonuclease MUS81-like, winged helix domain / EME1/MUS81, C-terminal ...EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Crossover junction endonuclease Mus81 / EME1/EME2, C-terminal domain / : / : / Crossover junction endonuclease MUS81-like, winged helix domain / EME1/MUS81, C-terminal / ERCC4 domain / ERCC4 domain / ERCC4 domain / Restriction endonuclease type II-like / DNA polymerase lambda lyase domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / ETHANOL / Crossover junction endonuclease EME1 / Crossover junction endonuclease MUS81
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsCollie, G.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Fragment-Based Discovery of Novel MUS81 Inhibitors.
Authors: Collie, G.W. / Borjesson, U. / Chen, Y. / Dong, Z. / Di Fruscia, P. / Gohlke, A. / Hoyle, A. / Hunt, T.A. / Jesani, M.H. / Luo, H. / Luptak, J. / Milbradt, A.G. / Narasimhan, P. / Packer, M. ...Authors: Collie, G.W. / Borjesson, U. / Chen, Y. / Dong, Z. / Di Fruscia, P. / Gohlke, A. / Hoyle, A. / Hunt, T.A. / Jesani, M.H. / Luo, H. / Luptak, J. / Milbradt, A.G. / Narasimhan, P. / Packer, M. / Patel, S. / Qiao, J. / Storer, R.I. / Stubbs, C.J. / Tart, J. / Truman, C. / Wang, A.T. / Wheeler, M.G. / Winter-Holt, J.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crossover junction endonuclease MUS81
B: Crossover junction endonuclease EME1
C: Crossover junction endonuclease MUS81
D: Crossover junction endonuclease EME1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,44611
Polymers140,6084
Non-polymers8387
Water4,576254
1
A: Crossover junction endonuclease MUS81
B: Crossover junction endonuclease EME1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7466
Polymers70,3042
Non-polymers4424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-28 kcal/mol
Surface area16050 Å2
2
C: Crossover junction endonuclease MUS81
D: Crossover junction endonuclease EME1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7005
Polymers70,3042
Non-polymers3963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-27 kcal/mol
Surface area15710 Å2
Unit cell
Length a, b, c (Å)70.574, 75.144, 83.011
Angle α, β, γ (deg.)90, 90.2, 90
Int Tables number4
Space group name H-MP1211

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Components

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Crossover junction endonuclease ... , 2 types, 4 molecules ACBD

#1: Protein Crossover junction endonuclease MUS81


Mass: 34159.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUS81 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96NY9, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters
#2: Protein Crossover junction endonuclease EME1 / MMS4 homolog / hMMS4


Mass: 36144.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EME1, MMS4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96AY2, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters

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Non-polymers , 4 types, 261 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-A1IA8 / 2-[2-[4-(cyanomethyl)phenyl]phenyl]-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid


Mass: 347.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H13N3O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG3350, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.02→55.68 Å / Num. obs: 56806 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.973 / Net I/σ(I): 4.3
Reflection shellResolution: 2.02→2.07 Å / Num. unique obs: 4183 / CC1/2: 0.273

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→55.71 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.176 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.163
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 2967 -RANDOM
Rwork0.2245 ---
obs0.2264 56789 99.6 %-
Displacement parametersBiso mean: 35.02 Å2
Baniso -1Baniso -2Baniso -3
1--5.8763 Å20 Å211.7033 Å2
2--0.5051 Å20 Å2
3---5.3712 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.02→55.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 59 254 5417
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085243HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.957121HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1790SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes880HARMONIC5
X-RAY DIFFRACTIONt_it5243HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion694SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4572SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion16.69
LS refinement shellResolution: 2.02→2.04 Å
RfactorNum. reflection% reflection
Rfree0.3722 80 -
Rwork0.3341 --
obs0.3368 1136 88.36 %

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