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- PDB-1xjv: Crystal structure of human POT1 bound to telomeric single-strande... -

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Basic information

Entry
Database: PDB / ID: 1xjv
TitleCrystal structure of human POT1 bound to telomeric single-stranded DNA (TTAGGGTTAG)
Components
  • Protection of telomeres 1
  • hT10 d(TTAGGGTTAG)
KeywordsTRANSCRIPTION/DNA / telomere / protein-DNA complex / single-stranded DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of DNA strand elongation / regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / regulation of double-strand break repair via nonhomologous end joining / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / positive regulation of helicase activity / telomerase inhibitor activity / DEAD/H-box RNA helicase binding ...positive regulation of DNA strand elongation / regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / regulation of double-strand break repair via nonhomologous end joining / 8-hydroxy-2'-deoxyguanosine DNA binding / 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 / positive regulation of DNA helicase activity / shelterin complex / Telomere C-strand synthesis initiation / Telomere C-strand (Lagging Strand) Synthesis / regulation of telomere maintenance via telomerase / negative regulation of telomerase activity / Processive synthesis on the C-strand of the telomere / nuclear telomere cap complex / G-rich strand telomeric DNA binding / positive regulation of telomere maintenance / single-stranded telomeric DNA binding / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / telomere capping / DNA duplex unwinding / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / telomere maintenance via 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 telomerase activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of telomere maintenance via telomerase / 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 / Protection of telomeres protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.73 Å
AuthorsLei, M. / Podell, E.R. / Cech, T.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structure of human POT1 bound to telomeric single-stranded DNA provides a model for chromosome end-protection
Authors: Lei, M. / Podell, E.R. / Cech, T.R.
History
DepositionSep 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / database_2
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
B: hT10 d(TTAGGGTTAG)
A: Protection of telomeres 1


Theoretical massNumber of molelcules
Total (without water)36,3122
Polymers36,3122
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.026, 103.243, 71.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: DNA chain hT10 d(TTAGGGTTAG)


Mass: 3115.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: Protein Protection of telomeres 1


Mass: 33197.074 Da / Num. of mol.: 1 / Fragment: splicing variant 2 (hPOT1V2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POT1 / Plasmid: pFASTBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q9NUX5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.44 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium sulfate, DTT, Sodium Chloride, Trisodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2NaClSodium chloride11
3sodium citrate11
4DTT11
5(NH4)2SO412
6NaClSodium chloride12
7sodium citrate12
8DTT12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11601
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211.107
SYNCHROTRONALS 8.2.221.0255, 1.0094, 1.0088, 0.9927
SYNCHROTRONALS 8.2.230.9067, 0.9206, 0.9202
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 23, 2003
ADSC QUANTUM 42CCDFeb 21, 2004
ADSC QUANTUM 43CCDFeb 21, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL SI(111)SINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL SI(111)MADMx-ray1
3DOUBLE CRYSTAL SI(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1071
21.02551
31.00941
41.00881
50.99271
60.90671
70.92061
80.92021
ReflectionResolution: 1.73→36.29 Å / Num. all: 38238 / Num. obs: 38238 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 28.838 Å2 / Rsym value: 0.041 / Net I/σ(I): 15.2
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 2.4 % / Num. unique all: 3053 / Rsym value: 0.474 / % possible all: 77.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.73→36.29 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.237 1839 random
Rwork0.228 --
all0.232 38238 -
obs0.232 36797 -
Refinement stepCycle: LAST / Resolution: 1.73→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 207 0 247 2766
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.39

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