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- PDB-7tuj: NMR solution structure of the phosphorylated MUS81-binding region... -

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Basic information

Entry
Database: PDB / ID: 7tuj
TitleNMR solution structure of the phosphorylated MUS81-binding region from human SLX4
ComponentsStructure-specific endonuclease subunit SLX4
KeywordsPROTEIN BINDING / SAP domain / disorder-to-order transition
Function / homology
Function and homology information


Slx1-Slx4 complex / positive regulation of t-circle formation / response to intra-S DNA damage checkpoint signaling / DNA double-strand break processing involved in repair via single-strand annealing / t-circle formation / telomeric D-loop disassembly / resolution of meiotic recombination intermediates / negative regulation of telomere maintenance via telomere lengthening / Resolution of D-loop Structures through Holliday Junction Intermediates / positive regulation of telomere maintenance ...Slx1-Slx4 complex / positive regulation of t-circle formation / response to intra-S DNA damage checkpoint signaling / DNA double-strand break processing involved in repair via single-strand annealing / t-circle formation / telomeric D-loop disassembly / resolution of meiotic recombination intermediates / negative regulation of telomere maintenance via telomere lengthening / Resolution of D-loop Structures through Holliday Junction Intermediates / positive regulation of telomere maintenance / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / nucleotide-excision repair / enzyme activator activity / chromosome, telomeric region / DNA replication / DNA repair / chromatin / DNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Structure-specific endonuclease subunit SLX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsPayliss, B.J. / Reichheld, S.E. / Lemak, A. / Arrowsmith, C.H. / Sharpe, S. / 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.J. / Tse, Y.W.E. / Reichheld, S.E. / Lemak, A. / Yun, H.Y. / Houliston, S. / Patel, A. / Arrowsmith, C.H. / Sharpe, S. / Wyatt, H.D.M.
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structure-specific endonuclease subunit SLX4


Theoretical massNumber of molelcules
Total (without water)9,9561
Polymers9,9561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study, T1/T2 method
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 Structure-specific endonuclease subunit SLX4 / BTB/POZ domain-containing protein 12


Mass: 9956.198 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLX4, BTBD12, KIAA1784, KIAA1987 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IY92
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CO)CA
151isotropic13D HNCO
161isotropic13D HNCA
191isotropic13D HN(CA)CB
181isotropic13D HBHA(CO)NH
171isotropic13D HNHA
1101isotropic13D 1H-15N TOCSY
1131isotropic13D 1H-13C NOESY aromatic
1121isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 500 uM [U-100% 13C; U-100% 15N] Phosphorylated MUS81-binding region of human SLX4, 25 mM sodium phosphate, 100 mM sodium chloride, 100 uM EDTA, 100 uM sodium azide, 93% H2O/7% D2O
Details: Sample prepared by phosphorylation with recombinant CDK1/Cyclin B to selectively phosphorylate three TP sites: T1544, T1561, and T1571. Specificity and stoichiometric phosphorylation of ...Details: Sample prepared by phosphorylation with recombinant CDK1/Cyclin B to selectively phosphorylate three TP sites: T1544, T1561, and T1571. Specificity and stoichiometric phosphorylation of these three sites were confirmed by mass spectrometry: LC-MS/MS and intact mass.
Label: 15N_13C_sample / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMPhosphorylated MUS81-binding region of human SLX4[U-100% 13C; U-100% 15N]1
25 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
100 uMEDTAnatural abundance1
100 uMsodium azidenatural abundance1
Sample conditionsIonic strength: 0.125 M / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
FMCGUILemak and Arrowsmithdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee, Tonelli, and Markleypeak picking
CcpNmr AnalysisCCPNpeak 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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