[English] 日本語
Yorodumi
- EMDB-42819: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42819
TitleSARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended
Map dataSARS-CoV-2 RNA SL5-6 domains with SL5c extended.
Sample
  • Complex: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended
    • RNA: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended
KeywordsSL5 / coronavirus / 5' UTR / RNA
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsKretsch RC / Xu L / Zheludev IN / Zhou X / Huang R / Nye G / Li S / Zhang K / Chiu W / Das R
Funding support United States, China, 11 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122579 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129541 United States
National Science Foundation (NSF, United States)GRFPDGE1656518 United States
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
Ministry of Science and Technology (MoST, China)2022YFA1302700 China
Other privateBioX Bowes fellowship United States
Other privateBioX Interdisciplinary Initiative Program United States
Other privateChEM-H COVID-19 Drug and Vaccine Prototyping seed grant United States
Department of Energy (DOE, United States)Coronavirus CARES Act United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)#U19AI171421 United States
CitationJournal: bioRxiv / Year: 2023
Title: Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.
Authors: Rachael C Kretsch / Lily Xu / Ivan N Zheludev / Xueting Zhou / Rui Huang / Grace Nye / Shanshan Li / Kaiming Zhang / Wah Chiu / Rhiju Das /
Abstract: Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to ...Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically-determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus SARS-CoV-2, resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T's "arms." Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4-6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across the studied human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9-8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4-9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities, with implications for potential protein-binding modes and therapeutic targets.
History
DepositionNov 14, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42819.png

Downloads & links

-
Map

FileDownload / File: emd_42819.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 RNA SL5-6 domains with SL5c extended.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.04 Å/pix.
x 256 pix.
= 522.24 Å		2.04 Å/pix.
x 256 pix.
= 522.24 Å		2.04 Å/pix.
x 256 pix.
= 522.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-1.679759 - 4.7597084
Average (Standard dev.)-0.0009129007 (±0.04931534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 522.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_42819_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of the SARS-CoV-2 RNA SL5-6 domains with SL5c extended.

Fileemd_42819_half_map_1.map
AnnotationHalf map of the SARS-CoV-2 RNA SL5-6 domains with SL5c extended.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of the SARS-CoV-2 RNA SL5-6 domains with SL5c extended.

Fileemd_42819_half_map_2.map
AnnotationHalf map of the SARS-CoV-2 RNA SL5-6 domains with SL5c extended.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended

EntireName: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended
Components
  • Complex: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended
    • RNA: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended

-
Supramolecule #1: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended

SupramoleculeName: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 65.7 KDa

-
Macromolecule #1: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended

MacromoleculeName: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5c extended
type: rna / ID: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: UGUCGUUGAC AGGACACGAG UAACUCGUCU AUCUUCUGCA GGCUGCUUAC GGUUUCGUCC GUGUUGCAGC CGAUCAUCAG CACAUCUAGG UUUCGUCCGG GUGUGACCCU GGGAAACCAG GGUAAGAUGG AGAGCCUUGU CCCUGGUUUC AACGAGAAAA CACACGUCCA ...String:
UGUCGUUGAC AGGACACGAG UAACUCGUCU AUCUUCUGCA GGCUGCUUAC GGUUUCGUCC GUGUUGCAGC CGAUCAUCAG CACAUCUAGG UUUCGUCCGG GUGUGACCCU GGGAAACCAG GGUAAGAUGG AGAGCCUUGU CCCUGGUUUC AACGAGAAAA CACACGUCCA ACUCAGUUUG CCUGUUUUAC AGGUUCGCGA CGUG

GENBANK: GENBANK: NC_045512.2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.31 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMNa-C8H18N2O4SSodium HEPES
10.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 5875 / Average exposure time: 1.19 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 813979
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Non-uniform Refinement / Number images used: 65937
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Ab initio reconstruction multi-class
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Non-uniform Refinement
Final 3D classificationNumber classes: 4 / Avg.num./class: 67428 / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Heterogeneous refinement
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

+
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