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- PDB-9f9k: Crystal structure of MUS81-EME1 bound by compound 15. -

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Basic information

Entry
Database: PDB / ID: 9f9k
TitleCrystal structure of MUS81-EME1 bound by compound 15.
Components
  • Crossover junction endonuclease EME1
  • Crossover junction endonuclease MUS81
KeywordsHYDROLASE / Endonuclease / fragment / drug discovery
Function / homology
Function and homology information


3'-flap endonuclease activity / resolution of mitotic recombination intermediates / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / endodeoxyribonuclease complex / double-stranded DNA endonuclease activity / Holliday junction resolvase complex / osteoblast proliferation / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates ...3'-flap endonuclease activity / resolution of mitotic recombination intermediates / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / endodeoxyribonuclease complex / double-stranded DNA endonuclease activity / Holliday junction resolvase complex / osteoblast proliferation / 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 / nuclear replication fork / replication fork processing / heterochromatin / replication fork / Fanconi Anemia Pathway / double-strand break repair / endonuclease activity / DNA repair / nucleolus / DNA binding / nucleoplasm / metal ion binding / nucleus
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
: / Structure-specific endonuclease subunit EME1 / Structure-specific endonuclease subunit MUS81
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.728 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)141,2738
Polymers140,6084
Non-polymers6654
Water00
1
A: Crossover junction endonuclease MUS81
B: Crossover junction endonuclease EME1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9696
Polymers70,3042
Non-polymers6654
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-29 kcal/mol
Surface area15080 Å2
MethodPISA
2
C: Crossover junction endonuclease MUS81
D: Crossover junction endonuclease EME1


Theoretical massNumber of molelcules
Total (without water)70,3042
Polymers70,3042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-9 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.264, 79.066, 84.836
Angle α, β, γ (deg.)90, 91.37, 90
Int Tables number4
Space group name H-MP1211

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Components

#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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1IA7 / 5-oxidanyl-6-oxidanylidene-2-(4-phenylphenyl)-1H-pyrimidine-4-carboxylic acid


Mass: 308.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
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: 12 % PEG8000, 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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.728→71.244 Å / Num. obs: 18360 / % possible obs: 72.6 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.041 / Rrim(I) all: 0.058 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.728-2.9663.30.5731.39190.6290.570.808116.5
8.334-71.2443.10.01926.39180.9990.0190.02697.9

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.728→71.24 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.383
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 873 -RANDOM
Rwork0.2327 ---
obs0.2338 18360 72.6 %-
Displacement parametersBiso mean: 70.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.1827 Å20 Å20.4603 Å2
2--0.6729 Å20 Å2
3----0.4902 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.728→71.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4871 0 48 0 4919
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074991HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.916780HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1693SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes838HARMONIC5
X-RAY DIFFRACTIONt_it4991HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion670SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3694SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion20.45
LS refinement shellResolution: 2.73→2.89 Å
RfactorNum. reflection% reflection
Rfree0.305 19 -
Rwork0.2858 --
obs0.2866 427 10.53 %

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