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- PDB-8u60: Structure of Mango II variant2 aptamer bound to T01-6A -

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Basic information

Entry
Database: PDB / ID: 8u60
TitleStructure of Mango II variant2 aptamer bound to T01-6A
ComponentsRNA Mango II variant 2 aptamer
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: 3.3 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 13, 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: RNA Mango II variant 2 aptamer
B: RNA Mango II variant 2 aptamer
C: RNA Mango II variant 2 aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,44318
Polymers35,7403
Non-polymers1,70415
Water905
1
A: RNA Mango II variant 2 aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4816
Polymers11,9131
Non-polymers5685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA Mango II variant 2 aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4816
Polymers11,9131
Non-polymers5685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA Mango II variant 2 aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4816
Polymers11,9131
Non-polymers5685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.374, 186.217, 104.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-103-

K

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Components

#1: RNA chain RNA Mango II variant 2 aptamer


Mass: 11913.234 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-VK0 / 2-[(~{E})-[6-(4-methoxyphenyl)-1-methyl-quinolin-4-ylidene]methyl]-3-methyl-1,3-benzothiazole


Mass: 411.539 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H23N2OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: Sodium malonate, polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3.3→45.51 Å / Num. obs: 5691 / % possible obs: 99.84 % / Redundancy: 12.3 % / Biso Wilson estimate: 53.24 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.67
Reflection shellResolution: 3.3→3.418 Å / Num. unique obs: 552 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
DIALS3.8data reduction
DIALS3.8data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→45.51 Å / SU ML: 0.4551 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2901 569 10.01 %
Rwork0.2406 5118 -
obs0.2445 5686 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.13 Å2
Refinement stepCycle: LAST / Resolution: 3.3→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2360 102 5 2467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152787
X-RAY DIFFRACTIONf_angle_d0.48844349
X-RAY DIFFRACTIONf_chiral_restr0.0229540
X-RAY DIFFRACTIONf_plane_restr0.0017116
X-RAY DIFFRACTIONf_dihedral_angle_d21.18361309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.630.33381390.27751262X-RAY DIFFRACTION100
3.63-4.160.32551380.28871240X-RAY DIFFRACTION99.78
4.16-5.230.31021430.23281277X-RAY DIFFRACTION100
5.24-45.510.24091490.20071339X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 19.1010989041 Å / Origin y: 25.274180055 Å / Origin z: -3.06328052995 Å
111213212223313233
T-0.44566933821 Å20.0262758793328 Å20.210807882278 Å2-0.42134244725 Å20.057937832925 Å2--0.554707122126 Å2
L1.36552525176 °2-0.245565964819 °2-0.0898956961308 °2-0.69358376848 °20.427615141625 °2--0.498174777499 °2
S-0.127196768174 Å °-0.294965157863 Å °-0.417052617585 Å °0.41537058509 Å °-0.0377595191791 Å °0.37978708834 Å °0.482541713138 Å °-0.24412245484 Å °-0.0317709873222 Å °
Refinement TLS groupSelection details: all

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