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- PDB-8d2a: Crystal structure of theophylline aptamer in complex with TAL3 -

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Basic information

Entry
Database: PDB / ID: 8d2a
TitleCrystal structure of theophylline aptamer in complex with TAL3
ComponentsRNA (33-MER)
KeywordsRNA / aptamer / theophylline
Function / homologyChem-QB3 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsMenichelli, E. / Spraggon, G.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Discovery of small molecules that target a tertiary-structured RNA.
Authors: Menichelli, E. / Lam, B.J. / Wang, Y. / Wang, V.S. / Shaffer, J. / Tjhung, K.F. / Bursulaya, B. / Nguyen, T.N. / Vo, T. / Alper, P.B. / McAllister, C.S. / Jones, D.H. / Spraggon, G. / ...Authors: Menichelli, E. / Lam, B.J. / Wang, Y. / Wang, V.S. / Shaffer, J. / Tjhung, K.F. / Bursulaya, B. / Nguyen, T.N. / Vo, T. / Alper, P.B. / McAllister, C.S. / Jones, D.H. / Spraggon, G. / Michellys, P.Y. / Joslin, J. / Joyce, G.F. / Rogers, J.
History
DepositionMay 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (33-MER)
B: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,02210
Polymers21,2752
Non-polymers7478
Water2,234124
1
A: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0115
Polymers10,6371
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0115
Polymers10,6371
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.075, 29.662, 80.291
Angle α, β, γ (deg.)95.390, 89.990, 109.010
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain RNA (33-MER)


Mass: 10637.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-QB3 / 6-methoxy-7-[(1-methylpiperidin-4-yl)methoxy]quinazolin-4-ol


Mass: 303.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium cacodylate, PEG 8000, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.17→27.91 Å / Num. obs: 9761 / % possible obs: 91.52 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 8.78
Reflection shellResolution: 2.17→2.248 Å / Num. unique obs: 911 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O15

1o15


Resolution: 2.17→27.91 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 514 5.28 %
Rwork0.1871 9216 -
obs0.1902 9730 91.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.52 Å2 / Biso mean: 39.6722 Å2 / Biso min: 13.74 Å2
Refinement stepCycle: final / Resolution: 2.17→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1408 92 124 1624
Biso mean--39.31 29.02 -
Num. residues----66
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.390.29851490.24892235238489
2.39-2.730.30931390.23642340247994
2.73-3.440.28491240.20412298242291
3.44-27.910.18621020.14552343244592
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03-0.0205-0.00680.0572-0.04720.04540.05820.0952-0.0501-0.17290.0142-0.18380.06580.02940.00010.2184-0.0070.01250.1847-0.01520.217812.7441-6.412-10.1763
20.205-0.08280.12910.23270.04030.1245-0.06250.13110.02030.05130.0505-0.05250.1316-0.139-0.07931.18330.23070.00370.4893-0.01590.205712.7897-14.6796-29.324
30.0731-0.1092-0.01340.28940.19710.21880.05270.00940.31580.0176-0.0493-0.070.00840.0130.01370.1465-0.01840.04140.22830.02670.26389.8077-3.203-8.4239
40.0085-0.00420.00440.0045-0.00220.0016-0.00810.049-0.0108-0.06350.1269-0.05030.0115-0.038100.1968-0.0085-0.01130.2436-0.00530.285421.4782-16.28148.2902
50.0310.0138-0.01290.03070.02380.0403-0.1812-0.21590.00530.45830.1438-0.0226-0.2438-0.2256-0.00790.52880.1105-0.01060.3997-0.03770.18338.0265-11.52328.912
60.05890.0507-0.00960.05910.0290.0583-0.00050.0213-0.0855-0.0532-0.0388-0.2210.1061-0.1304-0.00180.1929-0.0469-0.04870.1840.00010.253514.279-20.247712.2593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 20 )A11 - 20
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 33 )A21 - 33
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )B1 - 5
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 20 )B6 - 20
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 33 )B21 - 33

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