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- PDB-5h65: Crystal structure of human POT1 and TPP1 -

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Basic information

Entry
Database: PDB / ID: 5h65
TitleCrystal structure of human POT1 and TPP1
Components
  • Adrenocortical dysplasia protein homolog
  • Protection of telomeres protein 1
KeywordsDNA BINDING PROTEIN / telomere / OB fold
Function / homology
Function and homology information


positive regulation of single-stranded telomeric DNA binding / 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 / segmentation / urogenital system development / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding ...positive regulation of single-stranded telomeric DNA binding / 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 / segmentation / urogenital system development / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of double-strand break repair via nonhomologous end joining / positive regulation of helicase activity / protection from non-homologous end joining at telomere / 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 / : / positive regulation of telomere maintenance / nuclear telomere cap complex / single-stranded telomeric DNA binding / 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 / telomerase holoenzyme complex / embryonic limb morphogenesis / DNA duplex unwinding / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / telomere maintenance via telomerase / DNA polymerase binding / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / : / 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 / telomere maintenance / skeletal system development / intracellular protein transport / DNA Damage/Telomere Stress Induced Senescence / chromosome, telomeric region / nuclear body / protein-containing complex binding / nucleoplasm
Similarity search - Function
: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Adrenocortical dysplasia protein / 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 ...: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Adrenocortical dysplasia protein / 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, OB-fold
Similarity search - Domain/homology
Adrenocortical dysplasia protein homolog / Protection of telomeres protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsChen, C. / Wu, J. / Lei, M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into POT1-TPP1 interaction and POT1 C-terminal mutations in human cancer.
Authors: Chen, C. / Gu, P. / Wu, J. / Chen, X. / Niu, S. / Sun, H. / Wu, L. / Li, N. / Peng, J. / Shi, S. / Fan, C. / Huang, M. / Wong, C.C. / Gong, Q. / Kumar-Sinha, C. / Zhang, R. / Pusztai, L. / ...Authors: Chen, C. / Gu, P. / Wu, J. / Chen, X. / Niu, S. / Sun, H. / Wu, L. / Li, N. / Peng, J. / Shi, S. / Fan, C. / Huang, M. / Wong, C.C. / Gong, Q. / Kumar-Sinha, C. / Zhang, R. / Pusztai, L. / Rai, R. / Chang, S. / Lei, M.
History
DepositionNov 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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
A: Protection of telomeres protein 1
B: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8103
Polymers38,7452
Non-polymers651
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-31 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.231, 87.824, 87.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33305.375 Da / Num. of mol.: 1
Fragment: OB fold and Holiday Junction Like domain (UNP RESIDUES 341-634)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POT1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NUX5
#2: Protein Adrenocortical dysplasia protein homolog / POT1 and TIN2-interacting protein


Mass: 5439.225 Da / Num. of mol.: 1 / Fragment: POT1 binding motif (UNP RESIDUES 266-316)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACD, PIP1, PTOP, TINT1, TPP1 / Plasmid: pMAL-C2X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96AP0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.43 Å3/Da / Density % sol: 49.39 % / Mosaicity: 0.598 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 2.0 M NaH2PO4/K2HPO4 (2:3), 0.2 M sodium citrate, 0.1 M acetate pH 4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97876 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 22462 / % possible obs: 98.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 25.68 Å2 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.055 / Rrim(I) all: 0.141 / Χ2: 0.933 / Net I/av σ(I): 13.333 / Net I/σ(I): 5.2 / Num. measured all: 139163
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.185.20.61920990.8420.2830.6830.94593.6
2.18-2.265.70.56721610.860.2520.6221.0196
2.26-2.375.80.45221790.9010.2010.4960.94297.4
2.37-2.496.50.422220.9290.1670.4350.95898.5
2.49-2.656.70.32322520.9590.1340.350.96698.9
2.65-2.856.30.23122380.9710.0990.2520.96399.1
2.85-3.146.50.15522580.9870.0650.1680.9698.6
3.14-3.596.60.10222820.9920.0420.1111.00599.3
3.59-4.526.50.0723100.9940.0290.0760.89299.3
4.52-5060.05824610.9960.0250.0630.70399.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
PDB_EXTRACT3.2data extraction
HKL-3000data processing
HKL-3000data scaling
PHENIX1.9_1692phasing
PHENIX1.9_1692refinement
HKLdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.912 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.21
RfactorNum. reflection% reflection
Rfree0.2481 1107 5.17 %
Rwork0.196 --
obs0.1988 21417 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.15 Å2 / Biso mean: 30.643 Å2 / Biso min: 12.47 Å2
Refinement stepCycle: final / Resolution: 2.1→43.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 1 140 2815
Biso mean--31.73 31.06 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062730
X-RAY DIFFRACTIONf_angle_d1.1383704
X-RAY DIFFRACTIONf_chiral_restr0.066430
X-RAY DIFFRACTIONf_plane_restr0.004469
X-RAY DIFFRACTIONf_dihedral_angle_d13.3331012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.19560.29841110.2242033214477
2.1956-2.31130.29261140.22712292240686
2.3113-2.45610.25521510.22552516266795
2.4561-2.64580.2911360.222622275899
2.6458-2.9120.26861590.22462620277999
2.912-3.33320.29931470.22292658280599
3.3332-4.1990.23291420.17242717285999
4.199-43.92160.1851470.161428522999100

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