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

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Basic information

Entry
Database: PDB / ID: 2ziw
TitleCrystal structure of the Mus81-Eme1 complex
Components
  • Crossover junction endonuclease EME1
  • Mus81 protein
KeywordsHYDROLASE / Helix-hairpin-Helix / Alternative splicing / DNA damage / DNA recombination / DNA repair / Endonuclease / Magnesium / Metal-binding / Nuclease / Nucleus / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / 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 ...Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / 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 / Fanconi Anemia Pathway / double-strand break repair / endonuclease activity / nucleolus / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Crossover junction endonuclease EME1, DNA-binding domain / EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Rossmann fold - #10130 / Crossover junction endonuclease Mus81 / EME1/EME2, C-terminal domain / : / : ...Crossover junction endonuclease EME1, DNA-binding domain / EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Rossmann fold - #10130 / 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 / DNA polymerase; domain 1 / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Crossover junction endonuclease MUS81 / Crossover junction endonuclease MUS81 / Crossover junction endonuclease EME1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mus81 protein
B: Crossover junction endonuclease EME1


Theoretical massNumber of molelcules
Total (without water)73,6162
Polymers73,6162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-37.1 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.963, 88.963, 169.326
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 Mus81 protein / DNA structure specific endonuclease Mus81


Mass: 35333.582 Da / Num. of mol.: 1
Fragment: Nuclease domain and C-terminal domain, UNP residues 303-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mus81 / Plasmid: pCDF duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6GML8, UniProt: Q7SXA9*PLUS
#2: Protein Crossover junction endonuclease EME1 / hMMS4 / DNA repair protein Eme1


Mass: 38282.176 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
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Na-Acetate, 2.3M ammonium chloride, VAPOR DIFFUSION, HANGING DROP, pH 5.0, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 21889 / Num. obs: 21868 / % possible obs: 99.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 10.3 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.12 / Net I/σ(I): 52.3
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 9.4 / Num. unique all: 4031 / Rsym value: 0.267 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→37.56 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 123437.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1801 5.1 %RANDOM
Rwork0.272 ---
obs0.272 21599 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.1471 Å2 / ksol: 0.297352 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å27.84 Å20 Å2
2--2.44 Å20 Å2
3----4.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 0 0 3869
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 302 5.5 %
Rwork0.367 5164 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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