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- PDB-5we2: Structural Basis for Telomere Length Regulation by the Shelterin ... -

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Basic information

Entry
Database: PDB / ID: 5we2
TitleStructural Basis for Telomere Length Regulation by the Shelterin Bridge
Components
  • DNA-binding protein rap1
  • Protection of telomeres protein poz1
  • Protection of telomeres protein tpz1
KeywordsGENE REGULATION / Telomere / Shelterin / Cooperativity
Function / homology
Function and homology information


meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / telomere-telomerase complex assembly / mitotic telomere tethering at nuclear periphery / Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening ...meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / telomere-telomerase complex assembly / mitotic telomere tethering at nuclear periphery / Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / mitotic telomere maintenance via semi-conservative replication / shelterin complex / nuclear telomere cap complex / telomere capping / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / telomere organization / telomere maintenance / regulation of DNA-templated transcription / DNA binding / nucleus / cytosol
Similarity search - Function
S. pombe DNA-binding protein Rap1, C-terminal / Rap1, DNA-binding domain / Rap1, DNA-binding / TE2IP/Rap1 / Adrenocortical dysplasia protein / BRCT domain profile. / BRCT domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Protection of telomeres protein poz1 / Protection of telomeres protein tpz1 / DNA-binding protein rap1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, J.-K. / Liu, J. / Hu, X. / Sankaran, B. / Qiao, F.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for Shelterin Bridge Assembly.
Authors: Kim, J.K. / Liu, J. / Hu, X. / Yu, C. / Roskamp, K. / Sankaran, B. / Huang, L. / Komives, E.A. / Qiao, F.
History
DepositionJul 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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
B: Protection of telomeres protein tpz1
C: Protection of telomeres protein poz1
D: Protection of telomeres protein tpz1
F: DNA-binding protein rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9027
Polymers70,7715
Non-polymers1312
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-126 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.360, 95.390, 109.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 29749.180 Da / Num. of mol.: 2
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 / Production host: Escherichia coli (E. coli) / References: UniProt: O13852
#2: Protein/peptide Protection of telomeres protein tpz1 / Meiotically up-regulated gene 169 protein


Mass: 3964.574 Da / Num. of mol.: 2 / Fragment: UNP residues 476-508
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 / Production host: Escherichia coli (E. coli) / References: UniProt: O14246
#3: Protein/peptide DNA-binding protein rap1


Mass: 3343.561 Da / Num. of mol.: 1 / Fragment: UNP residues 467-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: rap1, SPBC1778.02 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96TL7
#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.: 34 / 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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 16-17% w/v PEG3350, 0.2-0.25 M Potassium citrate tribasic monohydrate, 0.1 M Tris-HCl, pH 8.3, 3% 1,5-Diaminopentane hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.999931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999931 Å / Relative weight: 1
ReflectionResolution: 2.5→83.33 Å / Num. obs: 30787 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Coot0.8model building
PHENIX1.9_1692phasing
MOSFLMdata processing
SCALAdata scaling
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: initial model from SAD phasing

Resolution: 2.5→45.666 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.58
RfactorNum. reflection% reflection
Rfree0.2626 2000 6.52 %
Rwork0.2093 --
obs0.2127 30695 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 2 34 4439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114529
X-RAY DIFFRACTIONf_angle_d1.2766063
X-RAY DIFFRACTIONf_dihedral_angle_d18.4091737
X-RAY DIFFRACTIONf_chiral_restr0.049640
X-RAY DIFFRACTIONf_plane_restr0.006770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.32231390.26932001X-RAY DIFFRACTION100
2.5625-2.63180.27311420.24872012X-RAY DIFFRACTION100
2.6318-2.70920.32611400.25352018X-RAY DIFFRACTION100
2.7092-2.79670.29671430.22642045X-RAY DIFFRACTION100
2.7967-2.89660.29561400.23092009X-RAY DIFFRACTION100
2.8966-3.01260.26921410.24462038X-RAY DIFFRACTION100
3.0126-3.14960.32631420.24582033X-RAY DIFFRACTION100
3.1496-3.31560.32141420.23582036X-RAY DIFFRACTION100
3.3156-3.52330.33191430.22732056X-RAY DIFFRACTION100
3.5233-3.79520.25161430.21052038X-RAY DIFFRACTION100
3.7952-4.17690.24341440.1932070X-RAY DIFFRACTION100
4.1769-4.78080.2161430.17642056X-RAY DIFFRACTION100
4.7808-6.02110.24871460.20172100X-RAY DIFFRACTION100
6.0211-45.67340.23361520.19242183X-RAY DIFFRACTION99

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