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- PDB-2i0q: Crystal structure of a telomere single-strand DNA-protein complex... -

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Basic information

Entry
Database: PDB / ID: 2i0q
TitleCrystal structure of a telomere single-strand DNA-protein complex from O. nova with full-length alpha and beta telomere proteins
Components
  • (Telomere-binding protein ...) x 2
  • 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
Keywordsstructural protein/DNA / SINGLE STRAND DNA-PROTEIN COMPLEX / structural protein-DNA COMPLEX
Function / homology
Function and homology information


telomere cap complex / telomerase inhibitor activity / regulation of telomere maintenance via telomerase / nuclear telomere cap complex / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / telomere capping / protein-containing complex / nucleus
Similarity search - Function
Telomere-binding Protein Beta Subunit; Chain B / Telomere-binding Protein Beta Subunit; Chain / Telomere-binding protein subunit beta / Telomere-binding protein, beta subunit domain superfamily / Telomere-binding protein beta subunit (TEBP beta) / Telomere-binding protein, alpha subunit, Spirotrichea / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 ...Telomere-binding Protein Beta Subunit; Chain B / Telomere-binding Protein Beta Subunit; Chain / Telomere-binding protein subunit beta / Telomere-binding protein, beta subunit domain superfamily / Telomere-binding protein beta subunit (TEBP beta) / Telomere-binding protein, alpha subunit, Spirotrichea / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Telomere-binding protein subunit beta / Telomere-binding protein subunit alpha
Similarity search - Component
Biological speciesSterkiella nova (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsHorvath, M.P. / Buczek, P.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova.
Authors: Buczek, P. / Horvath, M.P.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA
Authors: Horvath, M.P. / Schweiker, V.L. / Bevilacqua, J.M. / Ruggles, J.A. / Schultz, S.C.
#2: Journal: J.Mol.Biol. / Year: 2001
Title: DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex
Authors: Horvath, M.P. / Schultz, S.C.
History
DepositionAug 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
A: Telomere-binding protein alpha subunit
B: Telomere-binding protein beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,62412
Polymers101,1723
Non-polymers4529
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.331, 93.331, 423.779
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-684-

HOH

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Components

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DNA chain , 1 types, 1 molecules D

#1: DNA chain 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'


Mass: 3476.254 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 3'-terminal single strand DNA fragment from Oxytricha nova (Sterkiella nova) macronuclear telomeres

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Telomere-binding protein ... , 2 types, 2 molecules AB

#2: Protein Telomere-binding protein alpha subunit / Telomere-binding protein 56 kDa subunit / TEBP alpha


Mass: 56168.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sterkiella nova (eukaryote) / Gene: MAC-56A / Plasmid: pKKT7e / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P29549
#3: Protein Telomere-binding protein beta subunit / Telomere-binding protein 41 kDa subunit / TEBP beta


Mass: 41527.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sterkiella nova (eukaryote) / Gene: MAC-41A / Plasmid: pKKT7e / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P16458

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Non-polymers , 3 types, 315 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 21% (w/v) PEG-4000, 10% (v/v) ethylene glycol, 1.5 M sodium chloride, 40 mM MES, 2 mM DTT, 0.02% sodium azide, VAPOR DIFFUSION, HANGING DROP, pH 5.75, temperature 277.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG-400011
2ethylene glycol11
3sodium chloride11
4MES11
5DTT11
6sodium azide11
7H2O11
8PEG-400012
9sodium chloride12
10sodium azide12
11H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 86086 / Num. obs: 85120 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 47.6 Å2 / Rsym value: 0.041 / Net I/σ(I): 38.8
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.46 / % possible all: 95.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JB7

1jb7


Resolution: 1.91→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: Maximum likelihood refinement with intensities as target function (mli)
RfactorNum. reflection% reflectionSelection details
Rfree0.264 8402 9.9 %RANDOM; same test set as selected for 1JB7
Rwork0.243 ---
all0.245 86086 --
obs0.245 85003 98.7 %-
Solvent computationSolvent model: CNS SOLVE / Bsol: 30.2205 Å2 / ksol: 0.320563 e/Å3
Displacement parametersBiso mean: 43.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5455 231 24 309 6019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection obs% reflection obs (%)
1.91-2.030.342112999.70.32641334794.9
2.03-2.190.333113750.29971379098.1
2.19-2.410.326113890.29151409899.7
2.41-2.750.308213740.277214258100
2.75-3.470.272214830.247414416100
3.47-500.219414820.20731509499.7

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