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- PDB-5we1: Structural Basis for Shelterin Bridge Assembly -

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Basic information

Entry
Database: PDB / ID: 5we1
TitleStructural Basis for Shelterin Bridge Assembly
Components
  • Protection of telomeres protein poz1,Protection of telomeres protein poz1
  • Protection of telomeres protein tpz1
KeywordsGENE REGULATION / Telomere / Shelterin / Cooperativity
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 maintenance / telomere organization / 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: 3.202 Å
AuthorsKim, J.-K. / Liu, J. / Hu, X. / Yu, C. / Roskamp, K. / Sankaran, B. / Huang, L. / Komives, E.-A. / 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 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protection of telomeres protein poz1,Protection of telomeres protein poz1
B: Protection of telomeres protein tpz1
C: Protection of telomeres protein poz1,Protection of telomeres protein poz1
D: Protection of telomeres protein tpz1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6886
Polymers58,5584
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-142 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.110, 66.110, 123.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 25314.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast), (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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.0, 4% Reagent Alcohol, 0.3 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 3.2→57.25 Å / Num. obs: 9911 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.5
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Coot0.8model building
PHENIX1.9_1692phasing
MOSFLM7.2.1data processing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WE2

5we2


Resolution: 3.202→51.917 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 40.96
RfactorNum. reflection% reflection
Rfree0.3165 514 5.21 %
Rwork0.2664 --
obs0.2691 9872 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.202→51.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 2 0 3513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053589
X-RAY DIFFRACTIONf_angle_d1.2694798
X-RAY DIFFRACTIONf_dihedral_angle_d18.0871364
X-RAY DIFFRACTIONf_chiral_restr0.047500
X-RAY DIFFRACTIONf_plane_restr0.005599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2022-3.52440.43761080.33052369X-RAY DIFFRACTION99
3.5244-4.03420.43021420.2962313X-RAY DIFFRACTION99
4.0342-5.08190.25841240.26072366X-RAY DIFFRACTION100
5.0819-51.92420.28281400.23642310X-RAY DIFFRACTION99

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