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- PDB-7f6l: Crystal structure of human MUS81-EME2 complex -

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Basic information

Entry
Database: PDB / ID: 7f6l
TitleCrystal structure of human MUS81-EME2 complex
Components
  • Crossover junction endonuclease MUS81
  • Probable crossover junction endonuclease EME2
KeywordsDNA BINDING PROTEIN / MUS81 / EME2 / Endonuclease
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 / replication fork / Fanconi Anemia Pathway / double-strand break repair / endonuclease activity / DNA repair / nucleolus / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
: / 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 ...: / 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
Probable crossover junction endonuclease EME2 / Structure-specific endonuclease subunit MUS81
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHua, Z.K. / Zhang, D.P. / Yuan, C. / Lin, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31971222 China
CitationJournal: Structure / Year: 2022
Title: Crystal structure of the human MUS81-EME2 complex.
Authors: Hua, Z. / Fang, Q. / Zhang, D. / Luo, Z. / Yuan, C. / Lin, Z.
History
DepositionJun 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 18, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Probable crossover junction endonuclease EME2


Theoretical massNumber of molelcules
Total (without water)75,2412
Polymers75,2412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-37 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.097, 93.097, 87.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Crossover junction endonuclease MUS81


Mass: 34015.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUS81 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q96NY9, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters
#2: Protein Probable crossover junction endonuclease EME2


Mass: 41224.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EME2 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A4GXA9, 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 8% v/v TacsimateTM pH 7.0 and 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.199→29.44 Å / Num. obs: 12507 / % possible obs: 99.74 % / Redundancy: 13.8 % / CC1/2: 0.997 / Net I/σ(I): 16.63
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 1236 / CC1/2: 0.636

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-30001.13_2998data scaling
MOLREP1.13_2998phasing
Coot0.8.6.1model building
PHENIX1.13_2998model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p0p

4p0p


Resolution: 3.2→29.44 Å / SU ML: 0.4862 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 33.581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.283 610 -
Rwork0.229 11884 -
obs-12494 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4305 0 0 0 4305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01144385
X-RAY DIFFRACTIONf_angle_d1.64025950
X-RAY DIFFRACTIONf_chiral_restr0.0737688
X-RAY DIFFRACTIONf_plane_restr0.0265766
X-RAY DIFFRACTIONf_dihedral_angle_d9.8621599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.520.32221540.32312935X-RAY DIFFRACTION99.94
3.52-4.030.34421410.23562977X-RAY DIFFRACTION100
4.03-5.070.29181370.25052979X-RAY DIFFRACTION99.9
5.07-29.440.25991780.19382993X-RAY DIFFRACTION99.72

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