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

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Basic information

Entry
Database: PDB / ID: 1qzg
TitleCrystal structure of Pot1 (protection of telomere)- ssDNA complex
Components
  • Protection of telomeres protein 1
  • telomeric single-stranded DNA
KeywordsDNA BINDING Protein/DNA / protrein-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 / telomere capping / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding ...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 / telomere capping / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / 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
THYMIDINE-5'-PHOSPHATE / DNA / Protection of telomeres protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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 18, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
C: telomeric single-stranded DNA
D: telomeric single-stranded DNA
A: Protection of telomeres protein 1
B: Protection of telomeres protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2656
Polymers45,6204
Non-polymers6442
Water4,810267
1
C: telomeric single-stranded DNA
A: Protection of telomeres protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1323
Polymers22,8102
Non-polymers3221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: telomeric single-stranded DNA
B: Protection of telomeres protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1323
Polymers22,8102
Non-polymers3221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.741, 37.757, 106.785
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly in the asymmetric unitis generated by the following operation: matrix= ( 0.14029 0.00587 -0.99009 ) ( -0.02589 -0.99962 -0.00959 ) ( -0.98977 0.02698 -0.14009 ) translation= ( 64.45021 16.55769 73.96746 )

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Components

#1: DNA chain telomeric single-stranded DNA


Mass: 1535.047 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Protection of telomeres protein 1


Mass: 21275.020 Da / Num. of mol.: 2 / Fragment: residues 1-185
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: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: PEG5000MME, TRIS, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG500011
2MME11
3TRIS11
4H2O11
5PEG500012
6MME12
7TRIS12
8H2O12
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMtrisodium citrate1reservoirpH4.4
216-18 %PEG80001reservoir
35 mMdithiothreitol1reservoir
41
51
61
71
81

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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: 1.9→50 Å / Num. all: 32577 / Num. obs: 32234 / % possible obs: 93.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.97 Å / % possible all: 71.7
Reflection
*PLUS
Num. measured all: 103307 / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementResolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 948 random
Rwork0.223 --
obs0.223 31884 -
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 204 20 267 3184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.46

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