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- PDB-8d5l: Crystal structure of theophylline aptamer in complex with TAL1 -

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Basic information

Entry
Database: PDB / ID: 8d5l
TitleCrystal structure of theophylline aptamer in complex with TAL1
ComponentsRNA (33-MER)
KeywordsRNA / aptamer / theophylline
Function / homology4-amino-8-methylpteridine-2,7(1H,8H)-dione / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMenichelli, E. / Spraggon, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionJun 5, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,76123
Polymers42,5504
Non-polymers1,21119
Water9,818545
1
A: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9426
Polymers10,6371
Non-polymers3055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9426
Polymers10,6371
Non-polymers3055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9416
Polymers10,6371
Non-polymers3045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9355
Polymers10,6371
Non-polymers2984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.606, 50.271, 79.845
Angle α, β, γ (deg.)94.280, 91.530, 90.130
Int Tables number1
Space group name H-MP1

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Components

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RNA chain , 1 types, 4 molecules ABCD

#1: RNA chain
RNA (33-MER)


Mass: 10637.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 564 molecules

#2: Chemical
ChemComp-QIJ / 4-amino-8-methylpteridine-2,7(1H,8H)-dione


Mass: 193.163 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Calcium Acetate, PEG 3350

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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: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.64→41.06 Å / Num. obs: 46505 / % possible obs: 95.87 % / Redundancy: 3.2 % / CC1/2: 0.997 / Net I/σ(I): 8.3
Reflection shellResolution: 1.64→1.702 Å / Num. unique obs: 10593 / CC1/2: 0.877

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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: PDB entry 1O15

1o15


Resolution: 1.64→41.06 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 2165 4.67 %
Rwork0.1932 44224 -
obs0.1946 46389 95.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.28 Å2 / Biso mean: 27.8696 Å2 / Biso min: 10.44 Å2
Refinement stepCycle: final / Resolution: 1.64→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2816 99 545 3460
Biso mean--18.62 28.54 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.64-1.680.32811300.2807291794
1.68-1.720.27111370.248290894
1.72-1.770.31171440.2431287694
1.77-1.820.27561380.2328293494
1.82-1.880.24451290.2303294695
1.88-1.950.27411260.2193294195
1.95-2.030.24251350.2188288795
2.03-2.120.2361930.2069291595
2.12-2.230.25561750.2022286396
2.23-2.370.25661670.2134297797
2.37-2.550.30751320.219302997
2.55-2.810.27141440.208299398
2.81-3.220.1878930.1757304998
3.22-4.050.16351350.1526298797
4.05-41.060.16811870.1618300299
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)
10.02830.013-0.02990.02860.01230.04070.07530.0072-0.00450.0123-0.17260.0514-0.00290.0895-00.17520.0057-0.01760.1413-0.0040.18251.444513.786332.8705
20.03270.02610.010.0260.02760.0570.13690.05720.037-0.18730.10430.0984-0.0432-0.01320.15750.8154-0.0345-0.06970.26280.27790.21962.668928.013317.481
30.0783-0.022-0.00870.05690.02350.00110.0308-0.0552-0.0676-0.0321-0.01790.0740.03620.0278-0.00090.13760.0089-0.0110.0933-0.02110.19592.42914.55937.0314
40.0701-0.0069-0.02510.04910.06270.0408-0.04560.10760.0432-0.00950.0895-0.0395-0.1306-0.07530.00040.1611-0.02270.01450.25780.02680.14412.65454.394214.4866
50.0788-0.0591-0.01620.12260.12350.08650.00130.1674-0.0229-0.0512-0.034-0.03470.05170.0426-00.1455-0.02340.01530.25330.01770.171713.67660.759616.3329
60.0242-0.00310.02920.02730.03750.06190.0145-0.0078-0.0292-0.0603-0.09180.11070.0420.0452-00.1659-0.00060.02370.142-0.00570.171914.1831.693447.4902
70.0823-0.04640.00220.13380.00110.01980.136-0.0629-0.06440.05070.09880.02020.04480.05640.14450.68950.05390.04860.28530.21650.176913.968617.265562.6922
80.02210.02840.01120.04510.01360.00710.02390.04290.0203-0.0081-0.02040.07-0.03620.0545-0.00080.13720.00570.0130.1002-0.03120.171415.166230.898643.4048
90.0013-0.0055-0.00210.00130.00290.00310.02620.00180.0689-0.01020.0362-0.0243-0.05210.0008-00.12730.0075-0.00650.19540.0190.152932.200345.205652.0017
100.0077-0.0008-0.00790.00830.00710.0104-0.0865-0.10340.00960.04-0.05260.0416-0.0401-0.0238-0.01840.13080.0012-0.0130.3133-0.04330.13624.80145.465769.1368
110.0284-0.01740.01130.0114-0.00550.00680.1409-0.0962-0.07010.1777-0.00080.11250.1826-0.01970.0010.3222-0.0359-0.00930.41240.10960.234723.015834.355377.1825
120.0170.0047-0.01110.0010.00590.02330.04040.03220.11090.0139-0.07630.0077-0.0721-0.04-00.14830.0183-0.01230.1936-0.00780.194322.813347.38460.6057
130.0010.00250.00340.00170.00120.00380.021700.01340.01180.0504-0.0333-0.00220.0075-00.2002-0.0166-0.01540.16490.02910.214537.438152.484651.3929
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 15 )B1 - 15
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 33 )B16 - 33
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 10 )C1 - 10
7X-RAY DIFFRACTION7chain 'C' and (resid 11 through 20 )C11 - 20
8X-RAY DIFFRACTION8chain 'C' and (resid 21 through 33 )C21 - 33
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 5 )D1 - 5
10X-RAY DIFFRACTION10chain 'D' and (resid 6 through 10 )D6 - 10
11X-RAY DIFFRACTION11chain 'D' and (resid 11 through 20 )D11 - 20
12X-RAY DIFFRACTION12chain 'D' and (resid 21 through 30 )D21 - 30
13X-RAY DIFFRACTION13chain 'D' and (resid 31 through 33 )D31 - 33

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