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- PDB-2zix: Crystal structure of the Mus81-Eme1 complex -

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Basic information

Entry
Database: PDB / ID: 2zix
TitleCrystal structure of the Mus81-Eme1 complex
Components
  • Crossover junction endonuclease EME1
  • Crossover junction endonuclease MUS81
KeywordsHYDROLASE / Helix-hairpin-Helix / DNA damage / DNA recombination / DNA repair / Endonuclease / Magnesium / Metal-binding / Nuclease / Nucleus / Polymorphism / Alternative splicing / Phosphoprotein
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
ERCC4, Mus81-Eme1 complex, nuclease domain, subdomain 1 / ERCC4, Mus81-Eme1 complex, nuclease domain, subdomain 2 / Rubrerythrin, domain 2 - #10 / Crossover junction endonuclease EME1, DNA-binding domain / Invariant Chain; Chain I / EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Rubrerythrin, domain 2 ...ERCC4, Mus81-Eme1 complex, nuclease domain, subdomain 1 / ERCC4, Mus81-Eme1 complex, nuclease domain, subdomain 2 / Rubrerythrin, domain 2 - #10 / Crossover junction endonuclease EME1, DNA-binding domain / Invariant Chain; Chain I / EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Rubrerythrin, domain 2 / Crossover junction endonuclease Mus81 / EME1/EME2, C-terminal domain / : / : / Crossover junction endonuclease MUS81-like, winged helix domain / EME1/MUS81, C-terminal / YefM-like fold / ERCC4 domain / ERCC4 domain / ERCC4 domain / Restriction endonuclease type II-like / Other non-globular / DNA polymerase lambda lyase domain superfamily / Special / DNA polymerase; domain 1 / Few Secondary Structures / Irregular / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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: 3.5 Å
AuthorsChang, J.H. / Kim, J.J. / Choi, J.M. / Lee, J.H. / Cho, Y.
CitationJournal: Genes Dev. / Year: 2008
Title: Crystal structure of the Mus81-Eme1 complex
Authors: Chang, J.H. / Kim, J.J. / Choi, J.M. / Lee, J.H. / Cho, Y.
History
DepositionFeb 25, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)72,0542
Polymers72,0542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-38 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.814, 85.814, 176.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Crossover junction endonuclease MUS81 / DNA structure specific endonuclease Mus81


Mass: 34146.965 Da / Num. of mol.: 1
Fragment: Nuclease domain and C-terminal domain, UNP residues 246-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUS81 / Plasmid: pCDF duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96NY9, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters
#2: Protein Crossover junction endonuclease EME1 / hMMS4 / DNA repair protein Eme1


Mass: 37907.012 Da / Num. of mol.: 1
Fragment: Nuclease-like domain and C-terminal domain, UNP residues 246-570
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EME1 / Plasmid: pET duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96AY2, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M BTP, 1.25M Li2SO4, 100mM MgCl2, 2mM CdCl2, VAPOR DIFFUSION, HANGING DROP, pH 6.5, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 11204 / Num. obs: 10913 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.131 / Rsym value: 0.094 / Net I/σ(I): 17.1
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.6 / Num. unique all: 966 / Rsym value: 0.359 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZIU

2ziu


Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.821 / SU B: 20.698 / SU ML: 0.355 / Cross valid method: THROUGHOUT / ESU R Free: 0.869 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34554 441 4.8 %RANDOM
Rwork0.28524 ---
obs0.28815 8746 92.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.093 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å21.37 Å20 Å2
2--2.75 Å20 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 0 0 4154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224212
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.9735692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.8665519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.20423.264193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.53415755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4521544
X-RAY DIFFRACTIONr_chiral_restr0.1670.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023113
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.4110.23506
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3440.22763
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3780.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4250.2109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3610.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 25 -
Rwork0.438 483 -
obs--72.78 %

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