[English] 日本語
Yorodumi
- PDB-9cfn: Crystal structure of an exoribonuclease-resistant RNA from a Tomb... -

+
Open data


ID or keywords:

Loading...

-
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. / Hendrickson, W.A. / 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: To Be Published
Title: The structure of a nuclease-resistant infectious RNA element reveals common molecular strategies to evade host degradation machinery
Authors: Gezelle, J. / Korn, S.M. / McDonald, J. / Gong, Z. / Erickson, A. / Huang, C. / Cronin, M. / Yang, F. / Hendrickson, W.A. / Wimberly, B. / Steckelberg, A.L.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more