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- PDB-2mc3: NMR solution structure of the winged-helix domain from MUS81 stru... -

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Basic information

Entry
Database: PDB / ID: 2mc3
TitleNMR solution structure of the winged-helix domain from MUS81 structure-specific endonuclease
ComponentsMUS81 endonuclease homolog (Yeast), isoform CRA_b
KeywordsHYDROLASE / alpha beta / winged-helix / DNA binding
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 / replication fork / Fanconi Anemia Pathway / double-strand break repair / endonuclease activity / DNA repair / nucleolus / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
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 ...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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Crossover junction endonuclease MUS81 / Crossover junction endonuclease MUS81
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, SIMULATED ANNEALING
Model detailslowest energy, model1
AuthorsHarris, R. / Fadden, A. / Mcdonald, N.Q.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: A winged helix domain in human MUS81 binds DNA and modulates the endonuclease activity of MUS81 complexes.
Authors: Fadden, A.J. / Schalbetter, S. / Bowles, M. / Harris, R. / Lally, J. / Carr, A.M. / McDonald, N.Q.
History
DepositionAug 14, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Dec 7, 2016Group: Other
Revision 1.3Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MUS81 endonuclease homolog (Yeast), isoform CRA_b


Theoretical massNumber of molelcules
Total (without water)12,0071
Polymers12,0071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MUS81 endonuclease homolog (Yeast), isoform CRA_b / cDNA FLJ44872 fis / clone BRAMY2022320 / highly similar to Crossover junction endonuclease MUS81 (EC 3.1.22.-)


Mass: 12006.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_23303, MUS81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RECA- / References: UniProt: B3KX63, UniProt: Q96NY9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1143D 15N NOESY-HSQC
1223D 13C NOESY HSQC
1323D 13C AROMATIC NOESY-HSQ 2D IPAP
1442D 1H-15N HSQC
1522D 1H-13C HSQC
1613D HNCO
1722D 1H-13C AROMATIC HSQC
1832D IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM Na phosphate buffer, 250 mM NaCl, 1 mM EDTA, 1mM DTT, pH7.090% H2O/10% D2O
2MUS81-WINGED HELIX DOMAIN, 25 MM SODIUM PHOSPHATE, 250 MM SODIUM CHLORIDE, 1 MM EDTA, 1 MM DTT, pH7100% D2O
31 MM MUS81-WINGED HELIX DOMAIN, 25 MM SODIUM PHOSPHATE, 250 MM SODIUM CHLORIDE, 1 MM EDTA, 1 MM DTT, pH7, 5%n-octyl-penta(ethyleneglycol):octanol 0.96:190% H2O/10% D2O
41 MM MUS81-WINGED HELIX DOMAIN, 25 MM SODIUM PHOSPHATE, 250 MM SODIUM CHLORIDE, 1 MM EDTA, 1MM DTT pH790% H2O/10% D2O
Sample conditionsIonic strength: 250 / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: VARIAN UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER, A.T. ET AL.refinement
ANSIGBoucherstructure solution
RefinementMethod: SIMULATED ANNEALING, SIMULATED ANNEALING / Software ordinal: 1
Details: AB INITIO SIMULATED ANNEALING PROTOCOL WITHIN THE CNS PROGRAM, WITH PARALLHDGV5.3 FORCE FIELD AND PROLS NON-BONDED ENERGY FUNCTION. THIS PROTOCOL ADOPTS A MIXTURE OF CARTESIAN MOLECULAR ...Details: AB INITIO SIMULATED ANNEALING PROTOCOL WITHIN THE CNS PROGRAM, WITH PARALLHDGV5.3 FORCE FIELD AND PROLS NON-BONDED ENERGY FUNCTION. THIS PROTOCOL ADOPTS A MIXTURE OF CARTESIAN MOLECULAR DYNAMICS AND TORSION ANGLE DYNAMICS SIMULATE ANNEALING. INCLUDING RDC RESTRAINTS., AB INITIO SIMULATED ANNEALING PROTOCOL WITHIN THE CNS PROGRAM, WITH PARALLHDGV5.3 FORCE FIELD AND PROLS NON-BONDED ENERGY FUNCTION. THIS PROTOCOL ADOPTS A MIXTURE OF CARTESIAN MOLECULAR DYNAMICS AND TORSION ANGLE DYNAMICS SIMULATE ANNEALING. INCLUDING RDC RESTARINTS.
NMR constraintsNOE constraints total: 1634 / NOE intraresidue total count: 497 / NOE long range total count: 379 / NOE medium range total count: 357 / NOE sequential total count: 386 / Hydrogen bond constraints total count: 38 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 54
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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