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- PDB-7oav: Crystal structure of Chili RNA aptamer in complex with DMHBO+ (Ir... -

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Basic information

Entry
Database: PDB / ID: 7oav
TitleCrystal structure of Chili RNA aptamer in complex with DMHBO+ (Iridium III hexammine soaking crystal form)
ComponentsChili RNA Aptamer
KeywordsRNA / RNA aptamer / aptamer / Chili / fluorogenic RNA
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / : / : / DMHBO+ / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsMieczkowski, M. / Pena, V. / Hoebartner, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council (ERC)682586 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine.
Authors: Mieczkowski, M. / Steinmetzger, C. / Bessi, I. / Lenz, A.K. / Schmiedel, A. / Holzapfel, M. / Lambert, C. / Pena, V. / Hobartner, C.
History
DepositionApr 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chili RNA Aptamer
B: Chili RNA Aptamer
C: Chili RNA Aptamer
D: Chili RNA Aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,60124
Polymers67,7284
Non-polymers4,87320
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-67 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.192, 106.760, 63.552
Angle α, β, γ (deg.)90.000, 116.528, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A2 - 52
121chain 'A'A101
131chain 'A'A106
241(chain 'B' and (resid 2 through 34 or (resid 35...B2 - 52
251(chain 'B' and (resid 2 through 34 or (resid 35...B101
261(chain 'B' and (resid 2 through 34 or (resid 35...B106
371(chain 'C' and (resid 2 through 34 or (resid 35...C2 - 52
381(chain 'C' and (resid 2 through 34 or (resid 35...C101
391(chain 'C' and (resid 2 through 34 or (resid 35...C106
4101(chain 'D' and (resid 2 through 34 or (resid 35...D2 - 52
4111(chain 'D' and (resid 2 through 34 or (resid 35...D101
4121(chain 'D' and (resid 2 through 34 or (resid 35...D106

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Components

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RNA chain , 1 types, 4 molecules ABCD

#1: RNA chain
Chili RNA Aptamer


Mass: 16932.012 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 22 molecules

#2: Chemical
ChemComp-V5Z / DMHBO+ / [4-[(4Z)-4-[(3,5-dimethoxy-4-oxidanyl-phenyl)methylidene]-2-[(Z)-hydroxyiminomethyl]-5-oxidanylidene-imidazol-1-yl]phenyl]-trimethyl-azanium


Mass: 425.458 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H25N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ir
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, MES, Spermine tetrahydrochloride / PH range: 5.4 - 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.1048 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1048 Å / Relative weight: 1
ReflectionResolution: 2.85→46.14 Å / Num. obs: 15836 / % possible obs: 98.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 125.4 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.6
Reflection shellResolution: 2.85→3 Å / Rmerge(I) obs: 5.201 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2270 / CC1/2: 0.212 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OA3

7oa3


Resolution: 2.99→46.14 Å / SU ML: 0.5453 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.2894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 692 5.06 %
Rwork0.2015 12976 -
obs0.2039 13668 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 149.06 Å2
Refinement stepCycle: LAST / Resolution: 2.99→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4389 264 2 4655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235171
X-RAY DIFFRACTIONf_angle_d0.72318059
X-RAY DIFFRACTIONf_chiral_restr0.03081035
X-RAY DIFFRACTIONf_plane_restr0.0028223
X-RAY DIFFRACTIONf_dihedral_angle_d19.15122519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.220.47121550.44322555X-RAY DIFFRACTION97.31
3.22-3.540.36791310.32352598X-RAY DIFFRACTION97.85
3.54-4.060.28171480.25392551X-RAY DIFFRACTION98.54
4.06-5.110.26351290.2092599X-RAY DIFFRACTION98.73
5.11-46.140.2041290.15382673X-RAY DIFFRACTION99.12
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)
16.328065187062.47103589704-1.209152661972.423386624711.228637143512.468066506680.3125079230591.111439961080.6318203786440.3069421850270.437798187736-0.438216084527-0.4121204408040.202182975603-0.58250416051.181267235690.2155739456170.06491879840581.263765555830.20401050181.50751951725-21.19794497712.2467086613-7.00967619561
21.680811455231.500335736862.166870413471.710383067791.693438673173.390000982030.401080795733-0.0913566132924-0.1766785801860.335047195127-0.225125289349-0.182728592460.306519049721-1.000030761270.004189219850421.20998423286-0.0262617541330.1497878757051.38112579743-0.05923935610311.46151561257-4.00308728056-13.9542542847-7.6306751131
34.47414440434-3.098289611373.067595040221.50279557577-1.066656836991.285073056810.0139398370661-0.293175304054-0.5613451015180.2106833061180.3825217582960.417437860391-0.396265480061-0.0808399672241-0.1150878912621.335444668-0.110563143722-0.1109190994351.177329190670.0930931467651.37589086908-20.9651850627-14.655450582318.024154002
44.28275399323-2.69739044663-2.05163246871.324835697722.378332490024.427139939080.201151112845-0.04724973754130.519311635948-0.506631664586-0.1973539714510.2437547989290.333943107199-0.691051030412-0.01115452453711.49490463897-0.1025910324830.2047590992851.29937181344-0.1408164151731.67794769366-4.1680479801111.082689325718.7782473703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:102)
2X-RAY DIFFRACTION2(chain B and resseq 2:102)
3X-RAY DIFFRACTION3(chain C and resseq 2:102)
4X-RAY DIFFRACTION4(chain D and resseq 2:102)

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