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- PDB-9f9a: Crystal structure of MUS81-EME1 bound by compound 12. -

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Basic information

Entry
Database: PDB / ID: 9f9a
TitleCrystal structure of MUS81-EME1 bound by compound 12.
Components
  • Crossover junction endonuclease EME1
  • Crossover junction endonuclease MUS81
KeywordsHYDROLASE / MUS81-EME1 / fragment / inhibitor
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 / osteoblast proliferation / Holliday junction resolvase complex / endodeoxyribonuclease 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 / osteoblast proliferation / Holliday junction resolvase complex / endodeoxyribonuclease 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
: / Crossover junction endonuclease EME1 / Crossover junction endonuclease MUS81
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.911 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 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: Crossover junction endonuclease MUS81
F: Crossover junction endonuclease EME1
G: Crossover junction endonuclease MUS81
H: Crossover junction endonuclease EME1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,54020
Polymers281,2168
Non-polymers1,32312
Water00
1
A: Crossover junction endonuclease MUS81
B: Crossover junction endonuclease EME1
hetero molecules


  • defined by author&software
  • 70.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)70,6355
Polymers70,3042
Non-polymers3313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-25 kcal/mol
Surface area15570 Å2
MethodPISA
2
C: Crossover junction endonuclease MUS81
D: Crossover junction endonuclease EME1
hetero molecules


  • defined by author&software
  • 70.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)70,6355
Polymers70,3042
Non-polymers3313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-24 kcal/mol
Surface area15660 Å2
MethodPISA
3
E: Crossover junction endonuclease MUS81
F: Crossover junction endonuclease EME1
hetero molecules


  • defined by author&software
  • 70.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)70,6355
Polymers70,3042
Non-polymers3313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-28 kcal/mol
Surface area15730 Å2
MethodPISA
4
G: Crossover junction endonuclease MUS81
H: Crossover junction endonuclease EME1
hetero molecules


  • defined by author&software
  • 70.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)70,6355
Polymers70,3042
Non-polymers3313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-26 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.869, 124.348, 217.571
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Crossover junction endonuclease MUS81


Mass: 34159.898 Da / Num. of mol.: 4
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.: 4
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-A1IA6 / 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid


Mass: 282.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H10N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
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

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 20 % ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.911→83.166 Å / Num. obs: 40849 / % possible obs: 94.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 9.3
Reflection shellResolution: 2.911→3.226 Å / Num. unique obs: 2042 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.911→83.166 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / SU R Blow DPI: 2.084 / SU Rfree Blow DPI: 0.46 / SU Rfree Cruickshank DPI: 0.474 / Details: Actual overall B factor is 74.4
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 2051 -RANDOM
Rwork0.2429 ---
obs0.2447 40849 60.8 %-
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1--1.6022 Å20 Å20 Å2
2---0.8446 Å20 Å2
3---2.4468 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.911→83.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10001 0 92 0 10093
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710246HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9213912HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3511SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1727HARMONIC5
X-RAY DIFFRACTIONt_it10246HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1354SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7861SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion21.28
LS refinement shellResolution: 2.911→3.09 Å /
RfactorNum. reflection
Rfree0.4292 57
Rwork0.3275 -

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