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- PDB-9cfn: Crystal structure of an exoribonuclease-resistant RNA from a Tomb... -

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Basic information

Entry
Database: PDB / ID: 9cfn
TitleCrystal structure of an exoribonuclease-resistant RNA from a Tombusvirus-like associated RNA
ComponentsRNA (59-MER)
KeywordsRNA / xrRNA / pseudoknot
Function / homologyIRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciesBeet western yellows ST9 associated virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGezelle, J. / Wimberly, B. / Gong, Z. / Steckelberg, A.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-2036197 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150778 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: A conserved viral RNA fold enables nuclease resistance across kingdoms of life.
Authors: Gezelle, J.G. / Korn, S.M. / McDonald, J.T. / Gong, Z. / Erickson, A. / Huang, C.H. / Yang, F. / Cronin, M. / Kuo, Y.W. / Wimberly, B.T. / Steckelberg, A.L.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Structure summary / Category: audit_author / citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (59-MER)
B: RNA (59-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,13928
Polymers38,0252
Non-polymers7,11426
Water00
1
A: RNA (59-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,86415
Polymers19,0121
Non-polymers3,85214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (59-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,27513
Polymers19,0121
Non-polymers3,26312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.637, 42.392, 84.491
Angle α, β, γ (deg.)90.000, 103.620, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: RNA chain RNA (59-MER)


Mass: 19012.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beet western yellows ST9 associated virus
Production host: Beet western yellows ST9 associated virus / References: GenBank: 1782103816
#2: Chemical...
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50.07 % / Description: Rod-like cluster
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: well solution: 0.02 M Magnesium chloride hexahydrate 0.05 M Sodium cacodylate trihydrate pH 7.0 15% v/v 2-Propanol 0.001 M Hexammine cobalt(III) chloride 0.001 M Spermine 5 mg/mL RNA was ...Details: well solution: 0.02 M Magnesium chloride hexahydrate 0.05 M Sodium cacodylate trihydrate pH 7.0 15% v/v 2-Propanol 0.001 M Hexammine cobalt(III) chloride 0.001 M Spermine 5 mg/mL RNA was dissolved in: 2.5 mM MgCl2 10 mM HEPES-KOH pH 7.5 0.5 mM spermidine 300 nL sitting drops were set up using the mosquito with a 1:1 well:RNA ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→41.06 Å / Num. obs: 8421 / % possible obs: 87.25 % / Redundancy: 3.7 % / Biso Wilson estimate: 55.77 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.05966 / Rrim(I) all: 0.1177 / Net I/σ(I): 10.53
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.8365 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 494 / CC1/2: 0.817 / CC star: 0.948 / Rpim(I) all: 0.4913 / Rrim(I) all: 0.9738 / % possible all: 58.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOv3.352 5-Apr-2024data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→41.06 Å / SU ML: 0.3523 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2581 739 10.01 %
Rwork0.2173 6645 -
obs0.2214 7384 87.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2333 170 0 2503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172754
X-RAY DIFFRACTIONf_angle_d0.50344427
X-RAY DIFFRACTIONf_chiral_restr0.0246544
X-RAY DIFFRACTIONf_plane_restr0.0028109
X-RAY DIFFRACTIONf_dihedral_angle_d15.78161301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.120.36771040.2743932X-RAY DIFFRACTION62.26
3.12-3.440.2741300.21881173X-RAY DIFFRACTION78.02
3.44-3.940.28511640.24511477X-RAY DIFFRACTION97.27
3.94-4.950.26971690.21551512X-RAY DIFFRACTION99.94
4.96-41.060.21121720.19211551X-RAY DIFFRACTION98.18
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)
10.00951895657302-0.004427036297690.01222817570160.0028427342124-0.0118415857440.02336118781580.006476955693230.0020620958797-0.01690595600680.0281861585908-0.009001947886440.02055172301830.0506108300739-0.003198267823540.00828948687525-0.228688934973-0.178058789701-0.02952444888080.1260796180150.08332092921830.1751057088736.91136960351.6134814331131.2996178732
20.0157026216960.005666760124530.003991035716620.00298245824430.00123735745570.02139064821170.1854700455010.007263417857220.0925308203046-0.1079609418840.07503011308570.0660196545844-0.169226722512-0.0309208687852-0.0002511878016470.717990169427-0.08798171144830.1715611116740.6315478198860.07917051598530.48104398349641.16919725053.9546007044810.5532102573
30.0121009732823-0.0448262716088-0.03039990597370.3226739295890.2388789468370.1807324405460.1536210081010.110520667977-0.0399517612884-0.2406769408360.03454883655430.141716658157-0.161067356006-0.03913842741660.4549666933080.0761913395440.0904453815976-0.04327721486920.1425344519870.03103610761540.15262190775930.71327330376.9516037563125.6762573986
40.1037986983060.01324227430070.04426698665570.001371730553150.006509972912740.02188912781810.01432353948430.0450391292817-0.00422915524495-0.06081221208380.0824015605534-0.069341822108-0.0273629394395-0.04958105795420.01751245438221.305478412390.2213750958440.4509853378590.7467947976640.02735691521140.57627389947341.35000166221.675598106392.60088320094
50.045381309746-0.020439157708-0.02691328163290.007919778095480.01003797769340.0172694523772-0.0227767621747-0.01505121048630.0198623788845-0.00274686574018-0.07489133540040.0271835619799-0.0555770652701-0.0512538605939-0.04952561557910.05139985799490.0393896524206-0.09118151772940.182467820951-0.06471328788830.2475797895680.5763736125570.45497160396235.6417684126
60.07745882156830.00472721710418-0.04814266443770.0454599708627-0.02151648636640.03788229714440.0481943763477-0.0601735578064-0.0689273386215-0.01873903123940.1057545293990.0002587108063430.222609219447-0.001399397475930.0506827326480.7712531855970.0254484871655-0.2430487659330.579228429222-0.08178389634330.1909614316287.00398953606-1.1167050275315.649557839
70.2896801805080.0524333494135-0.04418558235380.0211325363178-0.0464945456490.499855478126-0.1494218188510.05780524058730.1443362857990.0248784803095-0.0568761977090.119765698583-0.0379985116436-0.10513369046-0.2457589480780.0970544230079-0.03608954984010.0001088445756190.227243101865-0.02608064639750.2086512020879.05890096785-4.1005796486934.1521851747
80.001426461891370.000604328130937-0.00361964677133-0.000578467772879-0.004176961633360.0156861389201-0.0717599207734-0.01789079695390.0660628528886-0.137908211174-0.1030573138970.108120205925-0.0564212590930.03096430689-6.48493493357E-50.937523131510.192858132188-0.06177213628790.8486711038140.03302235956490.50436429582410.7405330340.7848288911618.48908468714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )AA1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 22 )AA12 - 22
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 46 )AA23 - 46
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 55 )AA47 - 55
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 11 )BB2 - 11
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 22)BB12 - 22
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 46 )BB23 - 46
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 55 )BB47 - 55

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