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- PDB-7cui: Crystal structure of fission yeast Pot1 and Tpz1 -

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Basic information

Entry
Database: PDB / ID: 7cui
TitleCrystal structure of fission yeast Pot1 and Tpz1
Components
  • Protection of telomeres protein 1
  • Protection of telomeres protein tpz1
KeywordsDNA BINDING PROTEIN / telomere
Function / homology
Function and homology information


telomere-telomerase complex assembly / Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / mitotic telomere maintenance via semi-conservative replication / shelterin complex / regulation of telomere maintenance via telomerase / nuclear telomere cap complex / single-stranded telomeric DNA binding ...telomere-telomerase complex assembly / Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / mitotic telomere maintenance via semi-conservative replication / shelterin complex / regulation of telomere maintenance via telomerase / nuclear telomere cap complex / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / telomere capping / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / telomere maintenance / nucleus / cytosol
Similarity search - Function
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
Protection of telomeres protein 1 / Protection of telomeres protein tpz1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protection of telomeres protein 1
B: Protection of telomeres protein tpz1
C: Protection of telomeres protein 1
D: Protection of telomeres protein tpz1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0496
Polymers63,8574
Non-polymers1922
Water1,928107
1
A: Protection of telomeres protein 1
B: Protection of telomeres protein tpz1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0253
Polymers31,9292
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-20 kcal/mol
Surface area10690 Å2
MethodPISA
2
C: Protection of telomeres protein 1
D: Protection of telomeres protein tpz1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0253
Polymers31,9292
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-19 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.227, 126.227, 121.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-601-

SO4

21C-601-

SO4

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Components

#1: Protein Protection of telomeres protein 1


Mass: 22926.043 Da / Num. of mol.: 2
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: Protein Protection of telomeres protein tpz1 / Meiotically up-regulated gene 169 protein


Mass: 9002.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tpz1, mug169, SPAC6F6.16c, SPAC6F6.18c / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14246
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.81 Å3/Da / Density % sol: 67.69 % / Mosaicity: 0.18 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 8
Details: 25% PEG8000, 100 mM sodium citrate and 100 mM Tris-HCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL18U110.97853
SYNCHROTRONSSRF BL19U120.97853
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJun 29, 2016
DECTRIS PILATUS 6M2PIXELJun 29, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978531
21
ReflectionResolution: 2.6→50 Å / Num. obs: 30605 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 0.855 / Net I/σ(I): 5.6 / Num. measured all: 196899
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.695.50.6629860.7590.3030.7290.92198.7
2.69-2.86.50.57929800.8670.2450.630.91599.7
2.8-2.936.70.42330030.9350.1750.4580.91899.6
2.93-3.086.40.27730210.9650.1180.3020.88599.7
3.08-3.286.60.1930200.9840.080.2060.88499.8
3.28-3.536.80.12630450.9910.0520.1370.87199.8
3.53-3.886.70.08630580.9950.0360.0930.87299.9
3.88-4.456.40.05930710.9960.0250.0640.81299.8
4.45-5.66.70.0531260.9970.0210.0540.76799.9
5.6-506.10.04332950.9980.0190.0470.71899.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.6→43.78 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 17.901 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1482 4.9 %RANDOM
Rwork0.1956 ---
obs0.1977 28551 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.74 Å2 / Biso mean: 49.731 Å2 / Biso min: 17.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å2-0 Å2
2---0.84 Å2-0 Å2
3---1.67 Å2
Refinement stepCycle: final / Resolution: 2.6→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 10 107 3397
Biso mean--59.89 44.51 -
Num. residues----402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123368
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.634574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16522.84162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.17115586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1311516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022472
X-RAY DIFFRACTIONr_rigid_bond_restr133368
LS refinement shellResolution: 2.602→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 68 -
Rwork0.275 1669 -
all-1737 -
obs--78.35 %
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)
10.6945-0.37460.40132.1553-0.32522.3716-0.0102-0.046-0.05080.14050.141-0.09370.21970.2106-0.13080.12330.1009-0.03930.1574-0.02220.0222142.0512114.559-62.5186
24.9105-4.042-0.51464.93-2.4025.05930.2382-0.17590.5165-0.4496-0.1946-0.47120.44370.6206-0.04350.17660.1796-0.07990.2552-0.09480.2047151.2253105.5379-65.1843
31.00751.0418-0.62722.6833-0.55182.6381-0.06250.15980.0135-0.08860.1884-0.0374-0.24250.122-0.12590.0894-0.0880.01080.18860.0030.0089141.6381139.3391-90.0958
44.66210.9850.55121.3734-2.01233.97890.02230.4068-0.10310.2408-0.0912-0.0926-0.45960.43310.0690.1288-0.16130.02850.2819-0.07030.143151.4714147.7714-88.1849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A372 - 555
2X-RAY DIFFRACTION2B185 - 212
3X-RAY DIFFRACTION3C372 - 555
4X-RAY DIFFRACTION4D185 - 212

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