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- PDB-8u5z: Structure of Mango II variant aptamer bound to T01-7M-B -

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Basic information

Entry
Database: PDB / ID: 8u5z
TitleStructure of Mango II variant aptamer bound to T01-7M-B
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: 2.5 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

Downloads & links

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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)37,61016
Polymers35,6683
Non-polymers1,94213
Water1,56787
1
A: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1087
Polymers11,8891
Non-polymers2186
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7705
Polymers11,8891
Non-polymers8814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7314
Polymers11,8891
Non-polymers8423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.980, 181.080, 107.446
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.: 10 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 2 / Source method: obtained synthetically / Formula: C39H51N6O6S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Magnesium chloride hexahydrate, MOPS, TacsimateTM, hexamine cobalt (III) chloride

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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: 2.5→45.27 Å / Num. obs: 12754 / % possible obs: 97.99 % / Redundancy: 12.5 % / Biso Wilson estimate: 45.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.51
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 1213 / CC1/2: 0.903

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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: 2.5→45.27 Å / SU ML: 0.3479 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 1276 10.01 %
Rwork0.18 11473 -
obs0.1844 12749 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.16 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2370 87 87 2544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022749
X-RAY DIFFRACTIONf_angle_d0.57584279
X-RAY DIFFRACTIONf_chiral_restr0.0277537
X-RAY DIFFRACTIONf_plane_restr0.0036123
X-RAY DIFFRACTIONf_dihedral_angle_d18.40441353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.3661340.30071206X-RAY DIFFRACTION94.9
2.6-2.720.33531420.28541272X-RAY DIFFRACTION99.3
2.72-2.860.35241410.27111263X-RAY DIFFRACTION99.08
2.86-3.040.31361390.25671265X-RAY DIFFRACTION99.15
3.04-3.270.21671390.17831248X-RAY DIFFRACTION97.54
3.27-3.60.19521430.15181277X-RAY DIFFRACTION98.07
3.6-4.120.20691440.1611294X-RAY DIFFRACTION98.83
4.13-5.190.1871420.14551282X-RAY DIFFRACTION97
5.2-45.270.1721520.14831366X-RAY DIFFRACTION97.62
Refinement TLS params.Method: refined / Origin x: -16.4864640461 Å / Origin y: 25.2521957482 Å / Origin z: -3.03685615613 Å
111213212223313233
T0.219836046046 Å2-0.0231247085575 Å20.0461639606964 Å2-0.31865420686 Å20.00523872864762 Å2--0.360752846203 Å2
L0.887252927134 °2-0.456629589845 °20.112200250258 °2-0.715025032601 °2-0.244203020275 °2--0.585961330214 °2
S-0.0595398709834 Å °-0.103656090293 Å °-0.190940263435 Å °0.0615552855985 Å °0.0181852087475 Å °0.000301491758695 Å °0.14193800181 Å °-0.0181599626729 Å °0.031325524751 Å °
Refinement TLS groupSelection details: all

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