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- PDB-7oax: Crystal structure of the Chili RNA aptamer in complex with DMHBO+ -

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Basic information

Entry
Database: PDB / ID: 7oax
TitleCrystal structure of the Chili RNA aptamer in complex with DMHBO+
ComponentsChili RNA Aptamer
KeywordsRNA / RNA aptamer / aptamer / Chili / fluorogenic RNA
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / : / SPERMINE / DMHBO+ / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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)73,11634
Polymers67,7284
Non-polymers5,38830
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-61 kcal/mol
Surface area34530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.324, 100.352, 113.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 , 8 types, 67 molecules

#2: 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
#3: 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
#4: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293.15 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: 0.9998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.24→40.97 Å / Num. obs: 25428 / % possible obs: 94.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 61.21 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.3
Reflection shellResolution: 2.24→2.34 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1271 / % possible all: 91.5

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Processing

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

7oa3


Resolution: 2.24→40.97 Å / SU ML: 0.336 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 1269 5 %
Rwork0.2021 24114 -
obs0.204 25382 76.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.46 Å2
Refinement stepCycle: LAST / Resolution: 2.24→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4400 336 37 4773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00155246
X-RAY DIFFRACTIONf_angle_d0.56028138
X-RAY DIFFRACTIONf_chiral_restr0.02411036
X-RAY DIFFRACTIONf_plane_restr0.0019224
X-RAY DIFFRACTIONf_dihedral_angle_d14.94612568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.330.45410.4009768X-RAY DIFFRACTION22.29
2.33-2.440.5386540.37331054X-RAY DIFFRACTION30.63
2.44-2.570.3842830.33711556X-RAY DIFFRACTION45.04
2.57-2.730.40451630.36223097X-RAY DIFFRACTION89.66
2.73-2.940.36081820.3413455X-RAY DIFFRACTION99.81
2.94-3.230.30991820.26333483X-RAY DIFFRACTION99.7
3.23-3.70.29811830.23193490X-RAY DIFFRACTION99.22
3.7-4.660.20531860.1653533X-RAY DIFFRACTION99.87
4.66-40.970.15531950.13693678X-RAY DIFFRACTION99.46
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)
15.91083938271-0.904745782455.007902698849.110800908611.341179071667.959472672520.514164855134-1.26447698691-0.36176474407-1.37043035377-0.3920738341761.087557096880.004183112860120.299535511355-0.3062997162660.695297044987-0.127257556748-0.1427098453010.844091678314-0.04587921725480.816271251801-2.89514312586-18.1895592466-25.0064865353
22.942956787291.154197097441.138365292423.404804969312.50294551473.73097089266-0.01987214809110.0692921089278-0.5509366558370.6870364640770.0990860827802-0.3926732216730.2685614907840.221953423681-0.1051450596030.5121755902420.09014509654690.05902423446940.369353260637-0.0002080803085540.4560427590111.3702252221-7.67555990141.2479309
39.265788166392.012401203661.579151825452.110599379950.5740751345693.30641522385-0.08382797668340.344428311284-0.5537360780881.778627343750.195900104451-0.3429116400440.6591638634480.629419234095-0.1024921720810.6188919896250.106921546966-0.03895265655610.3908352125990.03614778358380.54341626780717.1822966327-7.69160651596-0.0477556867486
41.34389704303-1.95032285766-3.14643850593.20980309474.86701270997.606283486720.2531749755470.766425346832-1.53306904275-1.74547718959-0.162525680464-0.829116343891-0.1232503115581.15573888756-0.274735070490.9975125387040.3246652259460.1462431267160.826469805094-0.2091726356970.77494627759611.7078993377-14.5555608402-16.1078025179
53.95775320561-3.39647502322-0.1250120402343.54462188474-1.691715564525.1970259664-0.259670907458-0.0478643500569-0.818400592551-0.05101185890120.217417066344-0.2448419676211.06329037339-0.644813032966-0.040812682260.653583514263-0.04886577092710.007204408684770.332889590685-0.108694928330.6888987966013.53447049282-18.2062596391-8.41304160215
64.764920600572.839594145664.131346534172.233059838142.790454765078.47383115768-0.6861269135380.468218094945-0.190526997874-0.6508411509850.5517393602390.789864569972-1.44620098551-0.3176954484130.1064862531870.8132146781610.0219799454587-0.2556920804230.863774052626-0.01464795963470.738225012025-7.97676192576-12.5599900533-28.2404424526
75.8291103106-1.161837012583.578244170133.72400635195-2.715977255437.573129857170.156082538183-0.417743502236-0.430749479552-0.3525858261040.2069065115170.1530911134020.310174171102-0.855291826581-0.3823836285270.334468312474-0.09067249658910.07263894472620.344463789948-0.003217070297920.327359761357-10.8959490794-8.257693309210.1796227779
81.458061102230.652795466404-0.6456429267351.872956691623.192234140197.948940891240.0700658437635-2.54144025268-2.163280524492.401299695340.2648420997111.28644827920.913878515562-0.284627410442-0.215344633940.770192294385-0.03079784025330.2049470699451.052143280390.4364152359140.769597703346-12.7793517095-13.584476329322.9398546805
93.51497595911-0.0290974237011.438665279334.25696951257-2.024179476768.27517202271-0.0765511371039-0.59358583658-0.04495099397560.180016170248-0.0237342931716-0.2988813883920.4212683954310.3927058967780.1436836741340.368847386996-0.00665854858263-0.002241731686950.3815106305360.06055160297330.441768561031-0.444222198233-15.583565340222.4026020754
103.78681219411-1.11410612707-2.991091375233.902787416262.551335028785.666419315520.126052458469-0.2126763603960.0974851965766-0.194050629719-0.04908429863240.00925273663136-0.1428177915220.278760344322-0.07361635993950.425196627407-0.0420325410214-0.04244400382310.2575798405550.01915491346050.30341934771510.307978122411.704829752311.9871514654
111.792353342230.6414317131211.690604100770.5003544051710.680843241481.615893913980.365259643884-2.043062621811.177272999311.26609982472-0.33454805248-0.202433734635-0.9311745160480.685843671808-0.1075373823261.12770765285-0.113180385102-0.07095402383970.847866614925-0.2216970204720.61238687818713.347067953716.853520402424.7835491102
125.8887033584-1.61636988606-2.910531746284.880550204453.389814607594.142473708-0.13069905957-0.343141358648-0.2820023297210.455384565282-0.2006398246530.197028068153-0.312723735923-0.5320383578980.2796400442440.56684854677-0.01498672183220.03961684758990.569666950064-0.03829297866980.4671232225640.37033245587118.019531403525.3870323024
132.125036145791.011324462610.2101105985415.09563783808-3.032015580313.01029296947-0.07911056605360.1191500144740.03950781354970.9008794785130.206274856985-0.207480235963-0.657218963833-0.474017180843-0.1406084156780.408561150690.136941573851-0.08114091099520.298087923987-0.02900410054220.311037599416-9.7316526869912.5406436601-5.28271459517
143.490966764131.55028217881.302377084412.00329028981-0.3293704992813.64308730092-0.2758545971562.337866500991.03989452061-2.371410691990.6131496392780.4907666943780.201572569664-1.28543051105-0.4394108459280.9850734275020.0890896991782-0.04054896308340.962259903650.2376330223970.630759743315-11.713698066416.9648891272-18.0677640877
152.705811884261.08043271842-0.6425725697563.37065754089-3.458919333944.42084655245-0.4410284076290.369064584315-0.435957667175-0.357593813565-0.0234063566108-1.02314335585-0.1431650103250.5323313705640.4725238997260.475862705758-0.01575062506440.06492015375360.461540758832-0.03079420368650.5447355423890.8536204612217.8421313959-18.7221068094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 31 )
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 36 )
5X-RAY DIFFRACTION5chain 'A' and (resid 37 through 46 )
6X-RAY DIFFRACTION6chain 'A' and (resid 47 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 36 )
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 52 )
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 31 )
11X-RAY DIFFRACTION11chain 'C' and (resid 32 through 36 )
12X-RAY DIFFRACTION12chain 'C' and (resid 37 through 52 )
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 31 )
14X-RAY DIFFRACTION14chain 'D' and (resid 32 through 36 )
15X-RAY DIFFRACTION15chain 'D' and (resid 37 through 52 )

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