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- PDB-8u5j: Structure of Mango III variant aptamer bound to T01-07M-B -

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Basic information

Entry
Database: PDB / ID: 8u5j
TitleStructure of Mango III variant aptamer bound to T01-07M-B
ComponentsMango III variant
KeywordsRNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPassalacqua, L.F.M. / Ferre-D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD.
Authors: Lu, X. / Passalacqua, L.F.M. / Nodwell, M. / Kong, K.Y.S. / Caballero-Garcia, G. / Dolgosheina, E.V. / Ferre-D'Amare, A.R. / Britton, R. / Unrau, P.J.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mango III variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6485
Polymers11,6891
Non-polymers9594
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.660, 55.660, 65.715
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

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Components

#1: RNA chain Mango III variant


Mass: 11688.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-W6F / 2-[(E)-(1,7-dimethylquinolin-4(1H)-ylidene)methyl]-3-{2,16-dioxo-20-[(3aR,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium


Mass: 763.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H51N6O6S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.01 M magnesium sulphate heptahydrate, 0.05 M sodium cacodylate trihydrate pH 6.0, 1.8 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→38.87 Å / Num. obs: 13366 / % possible obs: 99.58 % / Redundancy: 17.5 % / Biso Wilson estimate: 19.96 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.29
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 1304 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASER2.8.3phasing
DIALS3.8data reduction
DIALS3.8data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.87 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 1332 10 %
Rwork0.2011 11987 -
obs0.2051 13319 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 762 62 116 940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061965
X-RAY DIFFRACTIONf_angle_d1.16121490
X-RAY DIFFRACTIONf_chiral_restr0.0544188
X-RAY DIFFRACTIONf_plane_restr0.010642
X-RAY DIFFRACTIONf_dihedral_angle_d16.3661466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.27471300.2531163X-RAY DIFFRACTION99
1.76-1.830.28961330.24111176X-RAY DIFFRACTION99.02
1.83-1.920.2621280.22971183X-RAY DIFFRACTION99.32
1.92-2.020.25191340.22171185X-RAY DIFFRACTION99.55
2.02-2.140.25751290.22561175X-RAY DIFFRACTION99.62
2.14-2.310.2581270.20051195X-RAY DIFFRACTION99.47
2.31-2.540.25881350.23181206X-RAY DIFFRACTION99.93
2.54-2.910.25511320.22981193X-RAY DIFFRACTION99.85
2.91-3.660.18231360.17811227X-RAY DIFFRACTION100
3.66-38.870.23411480.17411284X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -18.0302315378 Å / Origin y: 17.2586091624 Å / Origin z: 5.68738769773 Å
111213212223313233
T0.177411846682 Å2-0.0253228630407 Å20.000878145361817 Å2-0.136917127424 Å2-0.0448269840053 Å2--0.124195296332 Å2
L2.12213108868 °21.00775978492 °20.586754758924 °2-1.68787917689 °2-1.17916029978 °2--1.93999737601 °2
S0.0425758098982 Å °-0.300257271148 Å °0.185038826887 Å °0.193622529668 Å °-0.178882689353 Å °-0.021765987543 Å °-0.165060483379 Å °0.142246594937 Å °0.0906785223628 Å °
Refinement TLS groupSelection details: all

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