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- PDB-4uyi: Crystal structure of the BTB domain of human SLX4 (BTBD12) -

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Basic information

Entry
Database: PDB / ID: 4uyi
TitleCrystal structure of the BTB domain of human SLX4 (BTBD12)
ComponentsSTRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX4
KeywordsHYDROLASE
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 / Fanconi Anemia Pathway / nucleotide-excision repair / 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 / OTHER / Resolution: 1.86 Å
AuthorsPinkas, D.M. / Sanvitale, C.E. / Strain-Damerell, C. / Fairhead, M. / Wang, D. / Tallant, C. / Cooper, C.D.O. / Sorrell, F.J. / Kopec, J. / Chaikuad, A. ...Pinkas, D.M. / Sanvitale, C.E. / Strain-Damerell, C. / Fairhead, M. / Wang, D. / Tallant, C. / Cooper, C.D.O. / Sorrell, F.J. / Kopec, J. / Chaikuad, A. / Fitzpatrick, F. / Pike, A.C.W. / Hozjan, V. / Ying, Z. / Roos, A.K. / Savitsky, P. / Bradley, A. / Nowak, R. / Filippakopoulos, P. / Krojer, T. / Burgess-Brown, N.A. / Marsden, B.D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: To be Published
Title: Crystal Structure of the Btb Domain of Human Slx4 (Btbd12)
Authors: Pinkas, D.M. / Sanvitale, C.E. / Strain-Damerell, C. / Fairhead, M. / Wang, D. / Tallant, C. / Cooper, C.D.O. / Sorrell, F.J. / Kopec, J. / Chaikuad, A. / Fitzpatrick, F. / Pike, A.C.W. / ...Authors: Pinkas, D.M. / Sanvitale, C.E. / Strain-Damerell, C. / Fairhead, M. / Wang, D. / Tallant, C. / Cooper, C.D.O. / Sorrell, F.J. / Kopec, J. / Chaikuad, A. / Fitzpatrick, F. / Pike, A.C.W. / Hozjan, V. / Ying, Z. / Roos, A.K. / Savitsky, P. / Bradley, A. / Nowak, R. / Filippakopoulos, P. / Krojer, T. / Burgess-Brown, N.A. / Marsden, B.D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionSep 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Atomic model
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX4


Theoretical massNumber of molelcules
Total (without water)16,7411
Polymers16,7411
Non-polymers00
Water1,67593
1
A: STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX4
x 6


Theoretical massNumber of molelcules
Total (without water)100,4446
Polymers100,4446
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
Buried area13260 Å2
ΔGint-123.3 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.490, 142.490, 50.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

21A-2016-

HOH

31A-2045-

HOH

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Components

#1: Protein STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX4 / BTB/POZ DOMAIN-CONTAINING PROTEIN 12 / SLX4


Mass: 16740.691 Da / Num. of mol.: 1 / Fragment: BTB DOMAIN (BTBD12), UNP RESIDUES 668-796 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IY92
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENGINEERED CRYSTALLIZATION EPITOPE MUTATIONS V729I AND L734E

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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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2M MAGNESIUM CHLORIDE, 25% PEG3350, 0.1M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.86→71.25 Å / Num. obs: 16697 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 30.75 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.1
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.86→71.245 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 835 5 %
Rwork0.1796 --
obs0.1804 16697 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.15 Å2
Refinement stepCycle: LAST / Resolution: 1.86→71.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 93 1071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011999
X-RAY DIFFRACTIONf_angle_d1.1711359
X-RAY DIFFRACTIONf_dihedral_angle_d14.418348
X-RAY DIFFRACTIONf_chiral_restr0.044158
X-RAY DIFFRACTIONf_plane_restr0.006175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.97650.2891320.2342633X-RAY DIFFRACTION100
1.9765-2.12920.2381440.20092612X-RAY DIFFRACTION100
2.1292-2.34340.22071280.18272640X-RAY DIFFRACTION100
2.3434-2.68260.22941350.18212641X-RAY DIFFRACTION100
2.6826-3.37970.1981600.19022619X-RAY DIFFRACTION100
3.3797-71.29730.1611360.16412717X-RAY DIFFRACTION100

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