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- PDB-7cuh: Crystal structure of fission yeast Pot1 and ssDNA -

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Basic information

Entry
Database: PDB / ID: 7cuh
TitleCrystal structure of fission yeast Pot1 and ssDNA
Components
  • Protection of telomeres protein 1
  • Telomere single-strand DNA
KeywordsDNA BINDING PROTEIN / telomere / protein-ssDNA 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, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Protection of telomeres protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSun, H. / Wu, Z. / Wu, J. / Lei, M.
CitationJournal: Plos Genet. / Year: 2022
Title: Structural insights into Pot1-ssDNA, Pot1-Tpz1 and Tpz1-Ccq1 Interactions within fission yeast shelterin complex.
Authors: Sun, H. / Wu, Z. / Zhou, Y. / Lu, Y. / Lu, H. / Chen, H. / Shi, S. / Zeng, Z. / Wu, J. / Lei, M.
History
DepositionAug 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Protection of telomeres protein 1
B: Telomere single-strand DNA


Theoretical massNumber of molelcules
Total (without water)45,1442
Polymers45,1442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-18 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.212, 65.903, 92.789
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


Mass: 39516.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: pot1, SPAC26H5.06 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O13988
#2: DNA chain Telomere single-strand DNA


Mass: 5627.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)

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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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5
Details: 20% PEG3350, 100 mM ammonium sulfate and 100 mM Bis-Tris

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL18U110.97791
SYNCHROTRONSSRF BL19U120.97853
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELMar 16, 2016
DECTRIS PILATUS 6M2PIXELMar 16, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.977911
20.978531
ReflectionResolution: 3→50 Å / Num. obs: 8002 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.059 / Rrim(I) all: 0.149 / Χ2: 0.961 / Net I/σ(I): 4.5 / Num. measured all: 49420
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.115.50.4947370.9060.2250.5450.98895.2
3.11-3.235.90.3997790.9380.1760.4370.94698.6
3.23-3.386.40.3277870.9670.1390.3560.95399.9
3.38-3.566.50.2287810.9890.0970.2480.997100
3.56-3.786.50.1927980.9870.0820.2090.999100
3.78-4.076.10.1567880.990.0680.171.0399.9
4.07-4.486.40.1118120.9930.0470.1210.992100
4.48-5.136.50.0938120.9950.0390.1020.95599.9
5.13-6.4660.0978250.9920.0430.1060.905100
6.46-505.90.0768830.9940.0340.0830.8599.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QZG, 4HIK

1qzg

4hik


Resolution: 3→46.44 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.833 / SU B: 61.272 / SU ML: 0.487 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.598 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2976 372 5 %RANDOM
Rwork0.2674 ---
obs0.2689 7049 92.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.72 Å2 / Biso mean: 71.424 Å2 / Biso min: 22.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--0.06 Å20 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 3→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 377 0 0 2899
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123007
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.5644148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1445303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5822.276145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46815466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3161517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022168
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 15 -
Rwork0.298 362 -
all-377 -
obs--65.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7044-1.79070.00451.41190.09140.1346-0.1059-0.2452-0.28590.05670.16950.1421-0.0336-0.0815-0.06360.01730.03140.00080.09740.0770.2210.1656-6.1753-17.4481
210.8447-2.77061.14151.24280.39171.4226-0.60950.1922-0.22840.11660.09310.253-0.0483-0.06020.51640.29240.0280.10080.2333-0.10920.287115.2374-7.7104-33.7371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 337
2X-RAY DIFFRACTION2B1 - 18

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