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- PDB-7s1t: Structure of the human POT1-TPP1 complex -

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Basic information

Entry
Database: PDB / ID: 7s1t
TitleStructure of the human POT1-TPP1 complex
Components
  • Adrenocortical dysplasia protein homolog
  • Protection of telomeres protein 1
KeywordsDNA BINDING PROTEIN / POT1 / Telomere
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 / G-rich single-stranded DNA binding / telomere assembly / segmentation / urogenital system development / regulation of double-strand break repair via nonhomologous end joining / protection from non-homologous end joining at telomere / 8-hydroxy-2'-deoxyguanosine DNA binding ...positive regulation of single-stranded telomeric DNA binding / positive regulation of DNA strand elongation / regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / segmentation / urogenital system development / regulation of double-strand break repair via nonhomologous end joining / protection from non-homologous end joining at telomere / 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 / positive regulation of DNA helicase activity / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / negative regulation of telomerase activity / nuclear telomere cap complex / single-stranded telomeric DNA binding / positive regulation of telomere maintenance / 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 / protein localization to chromosome, telomeric region / DNA duplex unwinding / 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 / positive regulation of telomerase activity / 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 / positive regulation of telomere maintenance via telomerase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAramburu, T. / Skordalakes, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: POT1-TPP1 binding stabilizes POT1, promoting efficient telomere maintenance.
Authors: Aramburu, T. / Kelich, J. / Rice, C. / Skordalakes, E.
History
DepositionSep 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protection of telomeres protein 1
D: Protection of telomeres protein 1
G: Protection of telomeres protein 1
J: Protection of telomeres protein 1
B: Adrenocortical dysplasia protein homolog
E: Adrenocortical dysplasia protein homolog
H: Adrenocortical dysplasia protein homolog
K: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,41312
Polymers181,1518
Non-polymers2624
Water0
1
A: Protection of telomeres protein 1
B: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3533
Polymers45,2882
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-39 kcal/mol
Surface area19100 Å2
MethodPISA
2
D: Protection of telomeres protein 1
E: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3533
Polymers45,2882
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-38 kcal/mol
Surface area19170 Å2
MethodPISA
3
G: Protection of telomeres protein 1
H: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3533
Polymers45,2882
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-38 kcal/mol
Surface area19120 Å2
MethodPISA
4
J: Protection of telomeres protein 1
K: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3533
Polymers45,2882
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-39 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.880, 70.980, 103.790
Angle α, β, γ (deg.)76.760, 84.610, 70.550
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35446.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POT1 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q9NUX5
#2: Protein
Adrenocortical dysplasia protein homolog / POT1 and TIN2-interacting protein


Mass: 9841.022 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACD, PIP1, PTOP, TINT1, TPP1 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q96AP0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5 and 3.0M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→36.44 Å / Num. obs: 36930 / % possible obs: 90 % / Redundancy: 5.9 % / CC1/2: 0.996 / Net I/σ(I): 9.32
Reflection shellResolution: 2.9→2.98 Å / Num. unique obs: 2747 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UN7

5un7


Resolution: 2.9→36.44 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 36.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3069 1845 5 %
Rwork0.2504 35078 -
obs0.2532 36923 89.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 276.88 Å2 / Biso mean: 76.1356 Å2 / Biso min: 27.36 Å2
Refinement stepCycle: final / Resolution: 2.9→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11776 0 4 0 11780
Biso mean--68.28 --
Num. residues----1504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.980.38761410.36892707284889
2.98-3.070.42031450.35572757290292
3.07-3.160.43161460.32672769291592
3.16-3.280.36681430.32782723286690
3.28-3.410.34171400.29922676281689
3.41-3.560.39751330.28462525265883
3.56-3.750.32321430.26422713285691
3.75-3.990.32051450.25332756290192
3.99-4.290.32221420.22612710285291
4.29-4.730.24921340.21352546268084
4.73-5.410.28231490.21342825297494
5.41-6.80.2811410.24232670281189
6.81-36.440.23961430.21212701284490

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