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- PDB-8d5o: Crystal structure of theophylline aptamer in complex with TAL4 -

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Basic information

Entry
Database: PDB / ID: 8d5o
TitleCrystal structure of theophylline aptamer in complex with TAL4
ComponentsRNA (33-MER)
KeywordsRNA / aptamer / theophylline
Function / homologyChem-QEU / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9684
Polymers21,2752
Non-polymers6932
Water00
1
A: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9842
Polymers10,6371
Non-polymers3461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9842
Polymers10,6371
Non-polymers3461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.081, 29.535, 79.975
Angle α, β, γ (deg.)84.720, 90.030, 70.650
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 33)
21(chain B and resid 1 through 33)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Auth seq-ID: 1 - 33 / Label seq-ID: 1 - 33

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 1 through 33)AA
2(chain B and resid 1 through 33)BB

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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-QEU / 4-[4-(6,7-dimethoxyquinazolin-4-yl)piperazin-1-yl]butan-1-ol


Mass: 346.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26N4O3
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 277 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: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→39.96 Å / Num. obs: 4549 / % possible obs: 86.93 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.86 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.04389 / Rpim(I) all: 0.02679 / Rrim(I) all: 0.05151 / Net I/σ(I): 18.13
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 365 / CC1/2: 0.989

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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: 2.7→39.8 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2722 465 10.34 %
Rwork0.2378 4033 -
obs0.2413 4498 82.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.01 Å2 / Biso mean: 25.1637 Å2 / Biso min: 0.96 Å2
Refinement stepCycle: final / Resolution: 2.7→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1408 102 0 1510
Biso mean--25.52 --
Num. residues----66
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A784X-RAY DIFFRACTION1.351TORSIONAL
12B784X-RAY DIFFRACTION1.351TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-3.090.36141470.32261257140477
3.09-3.890.27581540.25431351150582
3.89-39.80.23021640.18771425158988
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)
10.87990.46111.2342.8346-0.58742.3185-0.08650.1722-0.0384-0.28660.1376-0.10520.0610.2430.02950.0762-0.02210.00480.08520.02620.1927-1.32379.2658-14.2594
20.4622-0.0721-0.3440.2371-0.43521.3150.05730.04070.0786-0.0331-0.0906-0.0842-0.17170.2370.05350.7956-0.20930.05130.49310.11050.25575.175915.423-32.8994
30.489-0.19110.03120.3883-0.15690.95270.14620.1475-0.1557-0.2025-0.16060.02480.10460.08470.03810.11740.0674-0.01050.10190.03870.277-1.0774.9826-12.186
41.62651.1692-0.25671.44920.18330.26210.105-0.1962-0.19080.2109-0.0352-0.05240.00120.0384-0.06990.0803-0.00670.0360.07440.01030.2110.62118.735910.3451
50.4850.08-0.44940.3233-0.37310.7044-0.0504-0.1395-0.0957-0.0303-0.0893-0.04630.18970.25270.17230.8696-0.22710.05940.47070.06570.24820.631210.436129.4368
61.56220.00490.88170.67150.25893.12540.0745-0.22350.25520.1233-0.0709-0.0003-0.07260.1040.0190.0576-0.04970.0240.11290.02130.22353.466521.88938.5504
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 10 )B1 - 10
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 20 )B11 - 20
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 33 )B21 - 33

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