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- PDB-6vwb: Solution structure of the N-terminal helix-hairpin-helix domain o... -

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Basic information

Entry
Database: PDB / ID: 6vwb
TitleSolution structure of the N-terminal helix-hairpin-helix domain of human MUS81
ComponentsCrossover junction endonuclease MUS81
KeywordsDNA BINDING PROTEIN / DNA repair / branched DNA structure
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 / nucleus / metal ion binding
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
Similarity search - Domain/homology
Crossover junction endonuclease MUS81
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsPayliss, B. / Houliston, S. / Lemak, A. / Arrowsmith, C.H. / Wyatt, H.D.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)156297 Canada
CitationJournal: Cell Rep / Year: 2022
Title: Phosphorylation of the DNA repair scaffold SLX4 drives folding of the SAP domain and activation of the MUS81-EME1 endonuclease
Authors: Payliss, B. / Houliston, S. / Lemak, A. / Arrowsmith, C.H. / Wyatt, H.D.M.
History
DepositionFeb 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crossover junction endonuclease MUS81


Theoretical massNumber of molelcules
Total (without water)10,6181
Polymers10,6181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Crossover junction endonuclease MUS81


Mass: 10618.409 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 (E. coli)
References: UniProt: Q96NY9, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCO
121isotropic23D HNCA
131isotropic23D HBHA(CO)NH
141isotropic23D CBCA(CO)NH
151isotropic12D 1H-15N HSQC
181isotropic12D 1H-13C HSQC aliphatic
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY aliphatic
191isotropic13D 1H-13C NOESY aromatic
1101isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 350 uM [U-13C; U-15N] Labeled Protein, 25 mM sodium phosphate, 100 mM sodium chloride, 100 uM EDTA, 95% H2O/5% D2O
Details: Basic conditions / Label: Double labeled / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 uMLabeled Protein[U-13C; U-15N]1
25 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
100 uMEDTAnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: basic conditions / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
ABACUSLemak and Arrowsmithchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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