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- PDB-5uso: Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ss... -

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Basic information

Entry
Database: PDB / ID: 5uso
TitleCrystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera (GGTTACrGrGrU)
Components
  • 7-9R_9mer DNA/RNA (5'-D(*GP*GP*TP*TP*AP*C)-R(P*GP*GP*U)-3')
  • Protection of telomeres protein 1
KeywordsDNA BINDING PROTEIN/DNA/RNA / Telomeres / OB-fold / DNA binding / DNA BINDING PROTEIN-DNA-RNA 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 / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping ...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 / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / 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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA/RNA hybrid / Protection of telomeres protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLloyd, N.R. / Wuttke, D.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1121842 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM-065103 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM059414 United States
CitationJournal: Structure / Year: 2018
Title: Discrimination against RNA Backbones by a ssDNA Binding Protein.
Authors: Lloyd, N.R. / Wuttke, D.S.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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: 7-9R_9mer DNA/RNA (5'-D(*GP*GP*TP*TP*AP*C)-R(P*GP*GP*U)-3')


Theoretical massNumber of molelcules
Total (without water)19,5432
Polymers19,5432
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-6 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.560, 57.610, 66.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protection of telomeres protein 1


Mass: 16721.908 Da / Num. of mol.: 1 / Fragment: UNP residues 199-337 / Mutation: V3D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: pot1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O13988
#2: DNA/RNA hybrid 7-9R_9mer DNA/RNA (5'-D(*GP*GP*TP*TP*AP*C)-R(P*GP*GP*U)-3')


Mass: 2820.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris, 0.2 mM sodium formate, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→66.76 Å / Num. obs: 13269 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 25.95 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.089 / Rrim(I) all: 0.201 / Net I/σ(I): 5.7 / Num. measured all: 62798 / Scaling rejects: 162
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.93-1.983.40.897281711770.5250.6561.3031.194.6
9.06-66.764.40.0786971580.9920.0410.08911.697.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.93 Å66.76 Å
Translation1.93 Å66.76 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
SCALA0.5.15data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HI4K

Resolution: 2→43.616 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1143 9.99 %
Rwork0.2104 --
obs0.2139 11441 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 187 0 120 1484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091431
X-RAY DIFFRACTIONf_angle_d0.991974
X-RAY DIFFRACTIONf_dihedral_angle_d22.887549
X-RAY DIFFRACTIONf_chiral_restr0.069206
X-RAY DIFFRACTIONf_plane_restr0.004219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.09120.32071380.2921238X-RAY DIFFRACTION93
2.0912-2.20150.3291370.2741254X-RAY DIFFRACTION93
2.2015-2.33940.34191340.27431177X-RAY DIFFRACTION88
2.3394-2.520.33191340.24221241X-RAY DIFFRACTION92
2.52-2.77360.25771400.22691250X-RAY DIFFRACTION93
2.7736-3.17480.22751480.21561320X-RAY DIFFRACTION96
3.1748-3.99950.20291480.17261369X-RAY DIFFRACTION100
3.9995-43.62590.21551640.1871449X-RAY DIFFRACTION99

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