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- PDB-4zou: Crystal structure of the BTB domain of SLX4 -

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Basic information

Entry
Database: PDB / ID: 4zou
TitleCrystal structure of the BTB domain of SLX4
ComponentsStructure-specific endonuclease subunit SLX4
KeywordsHYDROLASE / telomere / t-loop / endonuclease / ALT
Function / homology
Function and homology information


Slx1-Slx4 complex / positive regulation of t-circle formation / DNA double-strand break processing involved in repair via single-strand annealing / response to intra-S DNA damage checkpoint signaling / t-circle formation / telomeric D-loop disassembly / resolution of meiotic recombination intermediates / positive regulation of telomere maintenance / Resolution of D-loop Structures through Holliday Junction Intermediates / negative regulation of telomere maintenance via telomere lengthening ...Slx1-Slx4 complex / positive regulation of t-circle formation / DNA double-strand break processing involved in repair via single-strand annealing / response to intra-S DNA damage checkpoint signaling / t-circle formation / telomeric D-loop disassembly / resolution of meiotic recombination intermediates / positive regulation of telomere maintenance / 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 / metal ion binding / cytosol
Similarity search - Function
Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 ...Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Structure-specific endonuclease subunit SLX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsWan, B. / Chen, Y. / Wu, J. / Liu, Y. / Lei, M.
CitationJournal: to be published
Title: The BTB domain is both a structural and functional pivot of the SLX4-nuclease complex
Authors: Wan, B. / Chen, Y. / Wu, J. / Liu, Y. / Lei, M.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)13,0231
Polymers13,0231
Non-polymers00
Water57632
1
A: Structure-specific endonuclease subunit SLX4

A: Structure-specific endonuclease subunit SLX4


Theoretical massNumber of molelcules
Total (without water)26,0452
Polymers26,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area2590 Å2
ΔGint-25 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.391, 96.391, 71.825
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-801-

HOH

21A-820-

HOH

31A-824-

HOH

41A-829-

HOH

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Components

#1: Protein Structure-specific endonuclease subunit SLX4 / BTB/POZ domain-containing protein 12


Mass: 13022.712 Da / Num. of mol.: 1 / Fragment: BTB domain (UNP RESIDUES 669-787)
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IY92
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 4-6% PEG 6000, 0.1 M HEPES, pH 7.6, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. obs: 11151 / % possible obs: 99.5 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.089 / Χ2: 1.078 / Net I/av σ(I): 37.125 / Net I/σ(I): 7.1 / Num. measured all: 187864
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.2312.40.80810460.627196.1
2.23-2.3215.80.77110880.65199.9
2.32-2.4217.90.5610850.6551100
2.42-2.5518.10.39711010.6791100
2.55-2.71180.27210960.6931100
2.71-2.9217.90.16511040.7331100
2.92-3.2117.80.11611160.8871100
3.21-3.6817.60.08911241.6751100
3.68-4.6317.10.0711562.4921100
4.63-10015.90.03712351.483199.3

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Processing

Software
NameVersionClassification
SCALEPACKdata reduction
PHENIXphasing
PDB_EXTRACT3.11data extraction
SCALEPACKdata scaling
PHENIX1.7_650refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.15→41.739 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 532 4.79 %
Rwork0.2011 --
obs0.203 11108 99.34 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.708 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 131.9 Å2 / Biso mean: 58.5748 Å2 / Biso min: 22.64 Å2
Baniso -1Baniso -2Baniso -3
1-7.0259 Å2-0 Å2-0 Å2
2--7.0259 Å20 Å2
3----14.0517 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 0 32 938
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)
10.07150.0093-0.10080.4182-0.16441.3130.1135-0.0455-0.05480.22150.04650.3342-0.9854-0.0730.02560.7834-0.0273-0.0350.3984-0.00010.383-48.5624-8.20385.897
20.09990.2153-0.39650.7917-0.35951.27220.04130.021-0.33360.0819-0.1848-0.1982-0.19860.43790.10550.3168-0.0641-0.03920.39390.02910.3536-37.9724-23.7563-0.6263
31.1780.1542-0.6782.632-1.42832.7923-0.262-0.4043-0.2556-0.5380.09390.02930.53110.54630.06850.4688-0.0047-0.00440.57380.03310.4381-37.7123-29.9235-8.157
41.71921.3303-0.86992.0735-1.42531.3102-0.2818-0.0363-0.2851-0.647-0.034-0.1970.35930.44980.13680.43120.0040.00960.82830.08030.4156-36.21-32.8142-2.8505
51.94-1.00550.0842.40930.47942.43480.18440.04250.4718-0.1703-0.1196-0.6085-0.77410.9799-0.06580.4728-0.1781-0.02890.60650.01560.4293-32.898-16.0126-2.4334
61.51190.49490.23592.3996-0.19691.0727-0.03740.55340.47480.0476-0.4562-0.6186-0.75750.2371-0.3510.7322-0.3531-0.0260.49690.15860.5631-32.1925-9.1205-8.7846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 669:684)A669 - 684
2X-RAY DIFFRACTION2chain 'A' and (resseq 685:714)A685 - 714
3X-RAY DIFFRACTION3chain 'A' and (resseq 715:732)A715 - 732
4X-RAY DIFFRACTION4chain 'A' and (resseq 733:739)A733 - 739
5X-RAY DIFFRACTION5chain 'A' and (resseq 740:757)A740 - 757
6X-RAY DIFFRACTION6chain 'A' and (resseq 758:787)A758 - 787

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