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- PDB-1qzh: Crystal structure of Pot1 (protection of telomere)- ssDNA complex -

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Basic information

Entry
Database: PDB / ID: 1qzh
TitleCrystal structure of Pot1 (protection of telomere)- ssDNA complex
Components
  • Protection of telomeres protein 1
  • telomeric single-stranded DNA
KeywordsDNA Binding Protein/DNA / protein-DNA complex / single-stranded telomeric DNA / DNA Binding Protein-DNA COMPLEX
Function / homology
Function and homology information


Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / shelterin complex / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping ...Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / shelterin complex / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance / nucleus / cytosol
Similarity search - Function
Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / 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 / Protection of telomeres protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLei, M. / Podell, E.R. / Baumann, P. / Cech, T.R.
CitationJournal: Nature / Year: 2003
Title: DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA
Authors: Lei, M. / Podell, E.R. / Baumann, P. / Cech, T.R.
History
DepositionSep 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
G: telomeric single-stranded DNA
H: telomeric single-stranded DNA
I: telomeric single-stranded DNA
J: telomeric single-stranded DNA
K: telomeric single-stranded DNA
L: telomeric single-stranded DNA
A: Protection of telomeres protein 1
B: Protection of telomeres protein 1
C: Protection of telomeres protein 1
D: Protection of telomeres protein 1
E: Protection of telomeres protein 1
F: Protection of telomeres protein 1


Theoretical massNumber of molelcules
Total (without water)138,59512
Polymers138,59512
Non-polymers00
Water3,117173
1
G: telomeric single-stranded DNA
A: Protection of telomeres protein 1


Theoretical massNumber of molelcules
Total (without water)23,0992
Polymers23,0992
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: telomeric single-stranded DNA
B: Protection of telomeres protein 1


Theoretical massNumber of molelcules
Total (without water)23,0992
Polymers23,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: telomeric single-stranded DNA
C: Protection of telomeres protein 1


Theoretical massNumber of molelcules
Total (without water)23,0992
Polymers23,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: telomeric single-stranded DNA
D: Protection of telomeres protein 1


Theoretical massNumber of molelcules
Total (without water)23,0992
Polymers23,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
K: telomeric single-stranded DNA
E: Protection of telomeres protein 1


Theoretical massNumber of molelcules
Total (without water)23,0992
Polymers23,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
L: telomeric single-stranded DNA
F: Protection of telomeres protein 1


Theoretical massNumber of molelcules
Total (without water)23,0992
Polymers23,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.614, 76.329, 140.130
Angle α, β, γ (deg.)90.00, 115.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain
telomeric single-stranded DNA


Mass: 1824.229 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Protein
Protection of telomeres protein 1


Mass: 21275.020 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: POT1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O13988
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2TRIS11
3H2O11
4PEG400012
5TRIS12
6H2O12
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH8.5
227-30 %PEG40001reservoir
35 mMdithiothreitol1reservoir
41
51
61

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0688 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2003
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0688 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 44215 / Num. obs: 43793 / % possible obs: 88.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.47 Å / % possible all: 78.2
Reflection
*PLUS
% possible obs: 89.4 % / Num. measured all: 132615 / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.283 2180 random
Rwork0.249 --
obs0.249 43598 -
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8134 726 0 173 9033
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.43

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