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- PDB-12ci: Structure of dopamine-binding aptamer, DGR-1A, in complex with do... -

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Basic information

Entry
Database: PDB / ID: 12ci
TitleStructure of dopamine-binding aptamer, DGR-1A, in complex with dopamine
ComponentsDGR-1A aptamer
KeywordsRNA / aptamer / SELEX / dopamine / L-DOPA / riboswitch
Function / homology: / L-DOPAMINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSiwik, S.H. / Batey, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152029 United States
CitationJournal: To Be Published
Title: Structural characterization of a dopamine-binding aptamer raised through scaffolded selection
Authors: Siwik, S.H. / Batey, R.T.
History
DepositionMar 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DGR-1A aptamer
B: DGR-1A aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,28426
Polymers52,7992
Non-polymers3,48524
Water81145
1
A: DGR-1A aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,08113
Polymers26,4001
Non-polymers1,68112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DGR-1A aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,20313
Polymers26,4001
Non-polymers1,80312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.033, 59.302, 67.817
Angle α, β, γ (deg.)90.000, 106.506, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: RNA chain DGR-1A aptamer


Mass: 26399.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-LDP / L-DOPAMINE / DOPAMINE


Mass: 153.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H11NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 11% v/v MPD, 8 mM hexaamine cobalt(III) chloride, 12 mM sodium chloride, 80 mM potassium chloride, 40 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 24, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 15514 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 43.07 Å2 / CC1/2: 0.945 / Rpim(I) all: 0.052 / Rrim(I) all: 0.096 / Net I/σ(I): 18.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 756 / CC1/2: 0.731 / CC star: 0.919 / Rpim(I) all: 0.448 / Rrim(I) all: 0.801 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→23.3 Å / SU ML: 0.4427 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.1296 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 1365 10 %random
Rwork0.2245 12290 --
obs0.2296 13655 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.38 Å2
Refinement stepCycle: LAST / Resolution: 2.59→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3498 158 45 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00474046
X-RAY DIFFRACTIONf_angle_d0.95846403
X-RAY DIFFRACTIONf_chiral_restr0.0398820
X-RAY DIFFRACTIONf_plane_restr0.0052166
X-RAY DIFFRACTIONf_dihedral_angle_d17.9621966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.680.40071360.34911228X-RAY DIFFRACTION99.49
2.68-2.790.40761360.33731225X-RAY DIFFRACTION99.34
2.79-2.920.41081380.32561240X-RAY DIFFRACTION99.21
2.92-3.070.38011360.30271232X-RAY DIFFRACTION98.35
3.07-3.260.3481330.2571178X-RAY DIFFRACTION96.26
3.26-3.510.26641340.21291202X-RAY DIFFRACTION96.81
3.51-3.870.25371340.20491225X-RAY DIFFRACTION97.49
3.87-4.420.21961380.18831237X-RAY DIFFRACTION98.92
4.42-5.560.21351400.17331256X-RAY DIFFRACTION98.8
5.56-23.30.21541400.18621267X-RAY DIFFRACTION98.05

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