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- PDB-8u5r: Structure of Mango II variant aptamer bound to T01-6A -

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Basic information

Entry
Database: PDB / ID: 8u5r
TitleStructure of Mango II variant aptamer bound to T01-6A
ComponentsMango II 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: 2.6 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 II variant
B: Mango II variant
C: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20618
Polymers35,6683
Non-polymers53815
Water91951
1
A: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1318
Polymers11,8891
Non-polymers2417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0465
Polymers11,8891
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0295
Polymers11,8891
Non-polymers1404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.929, 180.748, 106.248
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 Mango II variant


Mass: 11889.210 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Magnesium chloride hexahydrate, MOPS, Tacsimate, hexamine cobalt (III) chloride, and 1-propanol

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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: 2.6→45.8 Å / Num. obs: 11414 / % possible obs: 99.67 % / Redundancy: 12.3 % / Biso Wilson estimate: 43.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.83
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 1114 / CC1/2: 0.823

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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: 2.6→45.8 Å / SU ML: 0.3457 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 1140 10 %
Rwork0.1995 10261 -
obs0.2054 11401 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2370 15 51 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00132667
X-RAY DIFFRACTIONf_angle_d0.36364170
X-RAY DIFFRACTIONf_chiral_restr0.0198537
X-RAY DIFFRACTIONf_plane_restr0.0023108
X-RAY DIFFRACTIONf_dihedral_angle_d18.10471284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.35981380.3111244X-RAY DIFFRACTION98.86
2.72-2.860.32351400.29611265X-RAY DIFFRACTION99.79
2.86-3.040.36911410.27891271X-RAY DIFFRACTION99.93
3.04-3.270.22641390.19381249X-RAY DIFFRACTION99.64
3.27-3.60.21591420.17421269X-RAY DIFFRACTION99.72
3.6-4.120.24181430.18351289X-RAY DIFFRACTION99.51
4.13-5.20.20341440.17441296X-RAY DIFFRACTION99.59
5.2-45.80.21311530.18161378X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: -16.3593509683 Å / Origin y: 25.2150076653 Å / Origin z: -2.93813679284 Å
111213212223313233
T0.269718272856 Å2-0.0124827015595 Å20.0519996458417 Å2-0.281092361732 Å20.010568125155 Å2--0.251261017561 Å2
L1.04837052801 °2-0.296566513212 °20.019148808815 °2-1.09096531075 °2-0.263038115643 °2--0.522001310144 °2
S-0.0646261895079 Å °-0.0990403818507 Å °-0.188649503723 Å °0.0801328829195 Å °0.00325727104856 Å °-0.0891887859832 Å °0.16075211057 Å °-0.0328163482271 Å °0.0478306765568 Å °
Refinement TLS groupSelection details: all

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