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- PDB-4m7c: Crystal structure of the TRF2-binding motif of SLX4 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4m7c
TitleCrystal structure of the TRF2-binding motif of SLX4 in complex with the TRFH domain of TRF2
Components
  • Peptide from Structure-specific endonuclease subunit SLX4
  • Telomeric repeat-binding factor 2
KeywordsHYDROLASE REGULATOR / telomere / t-loop / endonuclease / ALT / TRANSCRIPTION / Endonuclease regulator / DNA
Function / homology
Function and homology information


Slx1-Slx4 complex / positive regulation of t-circle formation / axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / response to intra-S DNA damage checkpoint signaling / DNA double-strand break processing involved in repair via single-strand annealing / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication ...Slx1-Slx4 complex / positive regulation of t-circle formation / axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / response to intra-S DNA damage checkpoint signaling / DNA double-strand break processing involved in repair via single-strand annealing / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / negative regulation of t-circle formation / t-circle formation / telomeric D-loop disassembly / shelterin complex / resolution of meiotic recombination intermediates / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / anterograde axonal transport / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / regulation of telomere maintenance / Resolution of D-loop Structures through Holliday Junction Intermediates / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / axon cytoplasm / enzyme activator activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / positive regulation of nitric-oxide synthase activity / male germ cell nucleus / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / DNA Damage/Telomere Stress Induced Senescence / cellular senescence / cell junction / in utero embryonic development / DNA replication / chromosome, telomeric region / nuclear body / negative regulation of gene expression / DNA repair / positive regulation of gene expression / protein-containing complex binding / chromatin / enzyme binding / protein homodimerization activity / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / Telomere repeat-binding factor, dimerisation domain / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) ...Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / Telomere repeat-binding factor, dimerisation domain / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Homeobox-like domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Telomeric repeat-binding factor 2 / Structure-specific endonuclease subunit SLX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWan, B. / Chen, Y. / Wu, J. / Liu, Y. / Lei, M.
CitationJournal: Cell Rep / Year: 2013
Title: SLX4 Assembles a Telomere Maintenance Toolkit by Bridging Multiple Endonucleases with Telomeres
Authors: Wan, B. / Yin, J. / Horvath, K. / Sarkar, J. / Chen, Y. / Wu, J. / Wan, K. / Lu, J. / Gu, P. / Yu, E.Y. / Lue, N.F. / Chang, S. / Liu, Y. / Lei, M.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2
C: Peptide from Structure-specific endonuclease subunit SLX4
D: Peptide from Structure-specific endonuclease subunit SLX4


Theoretical massNumber of molelcules
Total (without water)49,8424
Polymers49,8424
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-37 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.591, 69.183, 118.078
Angle α, β, γ (deg.)90.000, 94.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Telomeric repeat-binding factor 2 / TTAGGG repeat-binding factor 2 / Telomeric DNA-binding protein


Mass: 23410.283 Da / Num. of mol.: 2 / Fragment: TRFH domain, UNP residues 45-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2, TRBF2, TRF2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15554
#2: Protein/peptide Peptide from Structure-specific endonuclease subunit SLX4 / BTB/POZ domain-containing protein 12


Mass: 1510.720 Da / Num. of mol.: 2 / Fragment: TRF2-binding motif, UNP residues 1014-1025
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IY92
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 10% PEG 4000, 0.1M HEPES, pH 7.4, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / 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: 2.05→100 Å / Num. obs: 32186 / % possible obs: 96.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.068 / Χ2: 1.906 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.123.70.28731141.291195.6
2.12-2.213.90.21632001.411195.7
2.21-2.313.90.17231901.573196.5
2.31-2.433.90.14531831.701196.8
2.43-2.583.90.12132191.905196.8
2.58-2.783.90.132022.011196.5
2.78-3.063.90.07732452.17197.1
3.06-3.513.90.05932132.27196.9
3.51-4.423.80.04532532.555197.3
4.42-1003.90.03633672.122198

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BU8

3bu8


Resolution: 2.05→44.86 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.522 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1609 5.1 %RANDOM
Rwork0.2141 ---
obs0.2165 31784 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.23 Å2 / Biso mean: 24.9856 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å21.52 Å2
2---0.27 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 0 271 3665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193445
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.9734626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3375412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83323.043161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96915671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.441534
X-RAY DIFFRACTIONr_chiral_restr0.0630.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022522
X-RAY DIFFRACTIONr_rigid_bond_restr4.30133445
X-RAY DIFFRACTIONr_sphericity_free30.179597
X-RAY DIFFRACTIONr_sphericity_bonded23.22353568
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 119 -
Rwork0.235 2177 -
all-2296 -
obs--95.51 %
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)
10.2658-0.1323-0.25270.19240.2560.38660.01380.0319-0.00740.02620.0095-0.0326-0.0053-0.0113-0.02330.06930.0279-0.02250.0225-0.00920.0146-7.6067-14.2646-47.777
20.08420.051-0.10870.0682-0.08170.1705-0.0128-0.0166-0.00390.0422-0.0094-0.0181-0.0168-0.00330.02220.0810.0341-0.02260.09820.00290.0135-20.1142-14.1748-11.0314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 244
2X-RAY DIFFRACTION2B45 - 244

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