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- PDB-7bu5: Crystal Structure of Human SLX4 and MUS81 -

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Basic information

Entry
Database: PDB / ID: 7bu5
TitleCrystal Structure of Human SLX4 and MUS81
Components
  • MUS81 endonuclease homolog (Yeast), isoform CRA_b
  • Structure-specific endonuclease subunit SLX4
KeywordsHYDROLASE / HhH domain / SAP domain / Telomere
Function / homology
Function and homology information


Slx1-Slx4 complex / positive regulation of t-circle formation / 3'-flap endonuclease activity / DNA double-strand break processing involved in repair via single-strand annealing / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / t-circle formation / telomeric D-loop disassembly ...Slx1-Slx4 complex / positive regulation of t-circle formation / 3'-flap endonuclease activity / DNA double-strand break processing involved in repair via single-strand annealing / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / t-circle formation / telomeric D-loop disassembly / resolution of meiotic recombination intermediates / positive regulation of telomere maintenance / 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 / negative regulation of telomere maintenance via telomere lengthening / enzyme activator activity / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / cell junction / DNA replication / chromosome, telomeric region / DNA repair / chromatin / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / 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 ...Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / 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 / 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 / DNA polymerase lambda lyase domain superfamily / SKP1/BTB/POZ domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
GLYCINE / Crossover junction endonuclease MUS81 / Structure-specific endonuclease subunit SLX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWan, B. / Wu, J. / Lei, M.
CitationJournal: To be published
Title: SLX4 control MUS81 endonuclease function in telomere through an intermolecular SAP domain
Authors: Wan, B. / Wu, J. / Lei, M.
History
DepositionApr 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Structure-specific endonuclease subunit SLX4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7774
Polymers18,6272
Non-polymers1502
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-9 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.118, 59.118, 86.425
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-1726-

HOH

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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


Mass: 11407.146 Da / Num. of mol.: 1 / Fragment: HhH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUS81, hCG_23303 / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3KX63
#2: Protein Structure-specific endonuclease subunit SLX4 / BTB/POZ domain-containing protein 12


Mass: 7219.599 Da / Num. of mol.: 1 / Fragment: SAP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLX4, BTBD12, KIAA1784, KIAA1987 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IY92
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.45 % / Mosaicity: 0.367 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 8.5
Details: 25% w/v PEG 3350, 0.1M SPG (succinic acid: sodium dihydrogen phosphate: glycine, 2: 7: 7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97983 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97983 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16333 / % possible obs: 99.6 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.033 / Χ2: 1.025 / Net I/σ(I): 19.8 / Num. measured all: 149691
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.869.30.25416241.0161100
1.86-1.949.30.17316131.0851100
1.94-2.039.30.1216041.0651100
2.03-2.139.30.08516461.0311100
2.13-2.279.40.06416291.0491100
2.27-2.449.30.05716260.9311100
2.44-2.699.20.05316420.9931100
2.69-3.089.10.0416411.0051100
3.08-3.889.20.02616541.0381100
3.88-508.20.02116541.036196.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→33.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.539 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.106 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.206 827 5.1 %RANDOM
Rwork0.1687 ---
obs0.1705 15476 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.68 Å2 / Biso mean: 36.653 Å2 / Biso min: 17.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.2 Å20 Å2
2---0.39 Å20 Å2
3---1.28 Å2
Refinement stepCycle: final / Resolution: 1.8→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 10 85 1218
Biso mean--54.48 45.79 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121159
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.6761556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0065131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.63217.16274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3081520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02894
X-RAY DIFFRACTIONr_rigid_bond_restr1.51231159
LS refinement shellResolution: 1.8→1.842 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.269 71 -
Rwork0.154 1112 -
obs--98.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4094-0.0566-0.06790.00920.01520.0396-0.02820.0105-0.02060.00160.00230.0079-0.00980.01620.02590.0183-0.005-0.00770.02780.00910.0197-1.212516.216-0.8563
20.2055-0.0896-0.03160.26660.10010.07650.01790.01360.0040.023-0.0090.0031-0.0146-0.0071-0.00890.0226-0.0010.00440.01650.00470.005417.343420.0374-8.1146
30000000000000000.0073000.007300.0073000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 87
2X-RAY DIFFRACTION2B1558 - 1606

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