[English] 日本語
Yorodumi
- PDB-9e9o: SARS-CoV-2 SL5 crystal structure Cesium derivative -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e9o
TitleSARS-CoV-2 SL5 crystal structure Cesium derivative
ComponentsRNA (101-MER)
KeywordsRNA / UTR / virus / coronavirus / 5' UTR / untranslated region / translation / control
Function / homology: / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.51 Å
AuthorsJones, C.P. / Ferre-D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Rna / Year: 2025
Title: Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.
Authors: Jones, C.P. / Ferre-D'Amare, A.R.
History
DepositionNov 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (101-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,58413
Polymers32,5321
Non-polymers1,05212
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.991, 95.991, 114.351
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: RNA chain RNA (101-MER)


Mass: 32532.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: in vitro transcription vector pT7-TP(deltai) (others)
References: GenBank: 2272523031
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cs
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.67 Å3/Da / Density % sol: 73.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 1.2-1.4 M sodium citrate, 0.1 M HEPES-NaOH, pH 6.5-7.5 reservoir mixed in ratios of 1:2, 1:1, or 2:1 with folded RNA solution containing 25 mM HEPES-KOH, pH 7.4, 150 mM KCl, 10 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.89173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89173 Å / Relative weight: 1
ReflectionResolution: 3.51→48 Å / Num. obs: 14771 / % possible obs: 99.6 % / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09173 / Net I/σ(I): 12.77
Reflection shellResolution: 3.51→3.636 Å / Rmerge(I) obs: 4.844 / Mean I/σ(I) obs: 0.52 / Num. unique obs: 1470 / CC1/2: 0.247

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.51→48 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 1476 10.03 %
Rwork0.1666 --
obs0.1709 14719 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.51→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2129 7 32 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052409
X-RAY DIFFRACTIONf_angle_d1.1733783
X-RAY DIFFRACTIONf_dihedral_angle_d19.9741205
X-RAY DIFFRACTIONf_chiral_restr0.047503
X-RAY DIFFRACTIONf_plane_restr0.00698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.51-3.620.34711340.36871182X-RAY DIFFRACTION97
3.62-3.750.32551420.29541195X-RAY DIFFRACTION100
3.75-3.90.32741370.28531187X-RAY DIFFRACTION100
3.9-4.080.3021320.27581209X-RAY DIFFRACTION100
4.08-4.30.25721400.25671218X-RAY DIFFRACTION100
4.3-4.560.26261260.23331233X-RAY DIFFRACTION100
4.57-4.920.30071320.22191181X-RAY DIFFRACTION100
4.92-5.410.25171360.18751221X-RAY DIFFRACTION100
5.41-6.190.2311320.17391207X-RAY DIFFRACTION100
6.2-7.790.17471280.14651201X-RAY DIFFRACTION100
7.81-480.15691370.11181209X-RAY DIFFRACTION100
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)
14.1027-2.2709-3.53561.03152.52534.1433-0.57230.99-0.74980.082-0.42530.60081.0603-0.9640.90331.39370.127-0.1671.7839-0.20931.79247.604831.125347.6555
23.2529-4.0793-3.76545.24553.41951.81620.18540.8266-0.4459-0.245-0.68170.2381-0.2033-0.62970.68361.32760.3598-0.35091.9412-0.02121.913115.70337.491840.6915
31.58073.0721-2.05015.4434-2.15387.0606-0.10680.1210.27690.3062-0.0491.7687-0.8167-0.2784-0.02961.27260.5847-0.25151.6851-0.08281.7955.079550.163264.7974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 101 )

+
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