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- PDB-9c73: Hybrid G-quadruplex from Tetrahymena thermophila telomeric sequen... -

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Basic information

Entry
Database: PDB / ID: 9c73
TitleHybrid G-quadruplex from Tetrahymena thermophila telomeric sequence in complex with TrisQO
ComponentsG-quadruplex telomeric sequence
KeywordsDNA / G-quadruplex / TrisQO / hybrid
Function / homology: / : / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsAli, A. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: To Be Published
Title: Hybrid G-quadruplex from Tetrahymena thermophila telomeric sequence in complex with triangular star shaped TrisQ ligand
Authors: Ali, A. / Yatsunyk, L.A.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-quadruplex telomeric sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,18619
Polymers7,9851
Non-polymers2,20118
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.913, 54.913, 98.701
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain G-quadruplex telomeric sequence


Mass: 7985.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)

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Non-polymers , 7 types, 51 molecules

#2: Chemical ChemComp-A1AVT / (5S)-6-oxo-6H-dipyrido[1,2-b:1',2'-j]quinolizino[3,2-f][2,8]phenanthroline-12,19-diium


Mass: 399.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H17N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M potassium chloride, 0.01 calcium chloride dihydrate, 0.05 M HEPES sodium pH 7.0, 10% v/v PEG 400

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Data collection

DiffractionMean temperature: 196 K / Ambient temp details: LIQUID NITROGEN / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.656→47.556 Å / Num. obs: 11080 / % possible obs: 100 % / Redundancy: 18.6 % / Biso Wilson estimate: 32.27 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.3
Reflection shellResolution: 1.656→1.684 Å / Redundancy: 15.2 % / Rmerge(I) obs: 4.554 / Num. unique obs: 528 / CC1/2: 0.572 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Coot0.8.9.2model building
autoPROCdata reduction
PHENIX1.19.2_4158phasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→27.46 Å / SU ML: 0.2116 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.4149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 578 5.24 %
Rwork0.2136 10462 -
obs0.2149 11040 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.2 Å2
Refinement stepCycle: LAST / Resolution: 1.66→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 531 140 33 704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088742
X-RAY DIFFRACTIONf_angle_d1.09751091
X-RAY DIFFRACTIONf_chiral_restr0.056999
X-RAY DIFFRACTIONf_plane_restr0.008226
X-RAY DIFFRACTIONf_dihedral_angle_d31.975328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.820.36851520.33952502X-RAY DIFFRACTION98.88
1.82-2.090.28541370.2532572X-RAY DIFFRACTION100
2.09-2.630.26161180.25842636X-RAY DIFFRACTION100
2.63-27.460.21871710.18922752X-RAY DIFFRACTION99.63
Refinement TLS params.Method: refined / Origin x: -1.19159440873 Å / Origin y: -22.285637134 Å / Origin z: -3.52150231103 Å
111213212223313233
T0.178506745333 Å20.0119259841346 Å2-0.0301891881355 Å2-0.29366567765 Å2-0.0750054429368 Å2--0.264263948115 Å2
L4.79497271302 °20.321423918055 °20.778174291222 °2-4.20993875898 °20.732134063352 °2--4.81287137077 °2
S-0.146118695636 Å °-0.498092044623 Å °0.580158903709 Å °0.0433784143514 Å °-0.00918459357695 Å °0.0751112756031 Å °-0.484472991262 Å °-0.00357501229332 Å °0.0506563186904 Å °
Refinement TLS groupSelection details: all

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