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- PDB-3kjp: Crystal Structure of hPOT1V2-GGTTAGGGTTAG -

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Basic information

Entry
Database: PDB / ID: 3kjp
TitleCrystal Structure of hPOT1V2-GGTTAGGGTTAG
Components
  • 5'-D(*G*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3'
  • Protection of telomeres protein 1
KeywordsDNA BINDING PROTEIN/DNA / OB domain / Protein-DNA complex / Alternative splicing / Chromosomal protein / DNA-binding / Nucleus / Polymorphism / Telomere / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of DNA strand elongation / regulation of DNA helicase activity / positive regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / 8-hydroxy-2'-deoxyguanosine DNA binding / regulation of double-strand break repair via nonhomologous end joining / telomeric D-loop binding / positive regulation of helicase activity / telomerase inhibitor activity ...positive regulation of DNA strand elongation / regulation of DNA helicase activity / positive regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / 8-hydroxy-2'-deoxyguanosine DNA binding / regulation of double-strand break repair via nonhomologous end joining / telomeric D-loop binding / positive regulation of helicase activity / telomerase inhibitor activity / DEAD/H-box RNA helicase binding / establishment of protein localization to telomere / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / : / single-stranded telomeric DNA binding / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / DNA duplex unwinding / telomeric DNA binding / : / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of telomere maintenance via telomerase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / DNA Damage/Telomere Stress Induced Senescence / chromosome, telomeric region / nucleoplasm
Similarity search - Function
: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / 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) ...: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / 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 / DNA (> 10) / Protection of telomeres protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsNandakumar, J. / Cech, T.R. / Podell, E.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: How telomeric protein POT1 avoids RNA to achieve specificity for single-stranded DNA.
Authors: Nandakumar, J. / Podell, E.R. / Cech, T.R.
History
DepositionNov 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 1
B: 5'-D(*G*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)37,4982
Polymers37,4982
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-6 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.112, 104.198, 71.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21A-469-

HOH

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Components

#1: Protein Protection of telomeres protein 1 / hPot1 / POT1-like telomere end-binding protein


Mass: 33724.746 Da / Num. of mol.: 1 / Fragment: UNP residues 1-299
Source method: isolated from a genetically manipulated source
Details: Putative Splice variant of hPOT1 / Source: (gene. exp.) Homo sapiens (human) / Gene: POT1 / Plasmid: PFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q9NUX5
#2: DNA chain 5'-D(*G*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3'


Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 12mer synthetic single-stranded DNA containing human telomeric repeat sequence
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: AMMONIUM SULFATE, TRISODIUM CITRATE , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2009 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KOZHU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 35663 / Num. obs: 35271 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3331 / % possible all: 94.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
CNS1.2refinement
PDB_EXTRACT3.005data extraction
BOSdata collection softwaredata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XJV

1xjv


Resolution: 1.8→36.47 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 134195 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1697 5 %RANDOM SET that was used for structural solution of 1XJV
Rwork0.211 ---
all-35715 --
obs-33858 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.434 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 34.445 Å2 / Biso min: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å20 Å20 Å2
2--1.01 Å20 Å2
3----5.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 229 0 223 2777
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 239 5 %
Rwork0.292 4583 -
all-4822 -
obs-4592 82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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