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- PDB-5xxf: Crystal structure of Poz1, Tpz1 and Rap1 -

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Basic information

Entry
Database: PDB / ID: 5xxf
TitleCrystal structure of Poz1, Tpz1 and Rap1
Components
  • Protection of telomeres protein poz1
  • Protection of telomeres protein tpz1
  • Rap1
KeywordsDNA BINDING PROTEIN / telomere / sheterin / hub
Function / homology
Function and homology information


telomere-telomerase complex assembly / telomere cap complex / chromosome, telomeric repeat region / telomere maintenance via telomere lengthening / shelterin complex / telomere capping / telomerase holoenzyme complex / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere maintenance via telomerase ...telomere-telomerase complex assembly / telomere cap complex / chromosome, telomeric repeat region / telomere maintenance via telomere lengthening / shelterin complex / telomere capping / telomerase holoenzyme complex / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere maintenance via telomerase / telomere organization / telomere maintenance / DNA binding / nucleus / cytosol
Similarity search - Function
Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD
Similarity search - Domain/homology
Protection of telomeres protein poz1 / Protection of telomeres protein tpz1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsXue, J. / Chen, H. / Wu, J. / Lei, M.
CitationJournal: Cell Res. / Year: 2017
Title: Structure of the fission yeast S. pombe telomeric Tpz1-Poz1-Rap1 complex.
Authors: Xue, J. / Chen, H. / Wu, J. / Takeuchi, M. / Inoue, H. / Liu, Y. / Sun, H. / Chen, Y. / Kanoh, J. / Lei, M.
History
DepositionJul 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protection of telomeres protein poz1
C: Protection of telomeres protein tpz1
E: Rap1
B: Protection of telomeres protein poz1
D: Protection of telomeres protein tpz1
F: Rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5888
Polymers70,4576
Non-polymers1312
Water19811
1
A: Protection of telomeres protein poz1
C: Protection of telomeres protein tpz1
E: Rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2944
Polymers35,2283
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-68 kcal/mol
Surface area15450 Å2
MethodPISA
2
B: Protection of telomeres protein poz1
D: Protection of telomeres protein tpz1
F: Rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2944
Polymers35,2283
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-71 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.159, 85.741, 116.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protection of telomeres protein poz1 / Pot1-associated protein poz1


Mass: 29578.973 Da / Num. of mol.: 2 / Fragment: UNP residues 2-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: poz1, SPAC19G12.13c / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O13852
#2: Protein/peptide Protection of telomeres protein tpz1 / Meiotically up-regulated gene 169 protein


Mass: 3748.382 Da / Num. of mol.: 2 / Fragment: UNP residues 478-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tpz1, mug169, SPAC6F6.16c, SPAC6F6.18c / Plasmid: pMAL-C2X / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14246
#3: Protein/peptide Rap1


Mass: 1901.099 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.05 Å3/Da / Density % sol: 59.69 % / Mosaicity: 0.291 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 7 / Details: 0.2 M Potassium nitrate, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 15449 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Χ2: 0.949 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.216.20.7320.8190.320.8010.986100
3.21-3.346.80.4960.920.2050.5370.984100
3.34-3.496.80.3790.9430.1560.410.994100
3.49-3.686.70.2490.9730.1030.271.01100
3.68-3.916.60.1670.9870.070.1811.027100
3.91-4.216.20.120.9890.0530.1310.98100
4.21-4.636.80.0930.9940.0380.1010.982100
4.63-5.36.70.0830.9940.0340.090.937100
5.3-6.676.10.0750.9940.0320.0820.796100
6.67-506.10.0560.9960.0250.0610.7999.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XXE

5xxe


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.831 / SU B: 26.523 / SU ML: 0.466 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.543 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.3023 748 5 %RANDOM
Rwork0.2499 ---
obs0.2526 14259 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.39 Å2 / Biso mean: 71.445 Å2 / Biso min: 30.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0 Å2-0 Å2
2---0.14 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 2 11 4585
Biso mean--53.23 48.91 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194663
X-RAY DIFFRACTIONr_bond_other_d0.0030.024459
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9526246
X-RAY DIFFRACTIONr_angle_other_deg0.919310280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6095538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25724.385244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32215917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1831530
X-RAY DIFFRACTIONr_chiral_restr0.0640.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021124
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 46 -
Rwork0.319 862 -
all-908 -
obs--82.85 %

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