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- PDB-7cq4: Crystal structure of Slx1-Slx4 in complex with 5'flap DNA -

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Basic information

Entry
Database: PDB / ID: 7cq4
TitleCrystal structure of Slx1-Slx4 in complex with 5'flap DNA
Components
  • DNA (27-MER)
  • DNA (5'-D(*AP*GP*GP*AP*CP*AP*TP*CP*TP*TP*TP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*TP*TP*AP*CP*AP*AP*CP*AP*GP*AP*T)-3')
  • SLX4 isoform 1
  • Structure-specific endonuclease subunit SLX1
KeywordsHYDROLASE / endonuclease complex / Holliday Junction / SLX1-SLX4
Function / homology
Function and homology information


Slx1-Slx4 complex / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / double-strand break repair via homologous recombination / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
: / Structure-specific endonuclease subunit SLX1, C-terminal / Structure-specific endonuclease subunit Slx1 / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / : / Structure-specific endonuclease subunit SLX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.294 Å
AuthorsXu, X. / Wang, M. / Sun, J. / Li, G. / Yang, N. / Xu, R.M.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31521002 China
National Natural Science Foundation of China (NSFC)31870737 China
Ministry of Science and Technology (MoST, China)2019YFA0508900 China
Ministry of Science and Technology (MoST, China)2018YFA0107004 China
Ministry of Science and Technology (MoST, China)2017YFA0103304 China
National Natural Science Foundation of China (NSFC)31170704 China
National Natural Science Foundation of China (NSFC)31470719 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structure specific DNA recognition by the SLX1-SLX4 endonuclease complex.
Authors: Xu, X. / Wang, M. / Sun, J. / Yu, Z. / Li, G. / Yang, N. / Xu, R.M.
History
DepositionAug 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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
H: DNA (5'-D(*GP*GP*AP*TP*TP*AP*CP*AP*AP*CP*AP*GP*AP*T)-3')
K: DNA (5'-D(*AP*GP*GP*AP*CP*AP*TP*CP*TP*TP*TP*GP*CP*C)-3')
L: DNA (27-MER)
A: Structure-specific endonuclease subunit SLX1
B: SLX4 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0207
Polymers69,8895
Non-polymers1312
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-31 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.223, 123.223, 233.576
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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DNA chain , 3 types, 3 molecules HKL

#1: DNA chain DNA (5'-D(*GP*GP*AP*TP*TP*AP*CP*AP*AP*CP*AP*GP*AP*T)-3')


Mass: 4312.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: DNA chain DNA (5'-D(*AP*GP*GP*AP*CP*AP*TP*CP*TP*TP*TP*GP*CP*C)-3')


Mass: 4255.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: DNA chain DNA (27-MER)


Mass: 8291.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Protein , 2 types, 2 molecules AB

#4: Protein Structure-specific endonuclease subunit SLX1


Mass: 35884.621 Da / Num. of mol.: 1 / Mutation: Y17F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: SLX1, SCY_0436 / Plasmid: pCDF-Duet / Production host: Escherichia coli (E. coli)
References: UniProt: A6ZLG6, Hydrolases; Acting on ester bonds
#5: Protein SLX4 isoform 1


Mass: 17144.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLX4, GI526_G0003928 / Plasmid: pCDF-Duet / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PU22

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Non-polymers , 2 types, 14 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 0.1 M sodium cacodylate, pH 6.0, 12% PEG 1500 and 0.1 M TCEP hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.294→50 Å / Num. obs: 16540 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 96.37 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.039 / Rrim(I) all: 0.128 / Χ2: 1.003 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.4211.10.72215870.8870.2280.7580.98100
3.42-3.5511.10.62316220.8940.1960.6540.965100
3.55-3.7211.10.39916220.9590.1260.4191.015100
3.72-3.9111.10.29916070.9710.0940.3141.0299.9
3.91-4.1611.10.19816290.9880.0620.2081.05100
4.16-4.4811.10.14716460.9920.0460.1541.026100
4.48-4.9311.10.11716500.9940.0370.1230.954100
4.93-5.64110.11716750.9950.0370.1231.03100
5.64-7.110.70.11116910.9940.0350.1171100
7.1-509.90.0618110.9970.020.0640.98598

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7cq2

7cq2


Resolution: 3.294→48.314 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 849 5.15 %
Rwork0.2354 15647 -
obs0.2369 16496 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.84 Å2 / Biso mean: 90.05 Å2 / Biso min: 27.59 Å2
Refinement stepCycle: final / Resolution: 3.294→48.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 1119 2 12 4485
Biso mean--120.88 59.63 -
Num. residues----461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044684
X-RAY DIFFRACTIONf_angle_d0.9936533
X-RAY DIFFRACTIONf_chiral_restr0.043718
X-RAY DIFFRACTIONf_plane_restr0.004646
X-RAY DIFFRACTIONf_dihedral_angle_d20.351846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2942-3.50050.35571530.3108249999
3.5005-3.77070.31251510.28892544100
3.7707-4.150.31991510.26712545100
4.15-4.750.27891200.23482620100
4.75-5.98280.24981350.23862643100
5.9828-48.310.2111390.1954279699

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