+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42820 | ||||||||||||||||||||||||||||||||||||
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Title | SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5b extended | ||||||||||||||||||||||||||||||||||||
Map data | SARS-CoV-2 RNA SL5-6 domains with SL5b extended. | ||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | SL5 / coronavirus / 5' UTR / RNA | ||||||||||||||||||||||||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | ||||||||||||||||||||||||||||||||||||
Authors | Kretsch RC / Xu L / Zheludev IN / Zhou X / Huang R / Nye G / Li S / Zhang K / Chiu W / Das R | ||||||||||||||||||||||||||||||||||||
Funding support | United States, 11 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 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 severe-acute-respiratory-syndrome-related coronavirus 2 (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 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these 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 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 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 and notable differences, with implications for potential protein-binding modes and therapeutic targets. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42820.map.gz | 257.3 MB | EMDB map data format | |
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Header (meta data) | emd-42820-v30.xml emd-42820.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42820_fsc.xml | 17.8 KB | Display | FSC data file |
Images | emd_42820.png | 27.2 KB | ||
Masks | emd_42820_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-42820.cif.gz | 5.7 KB | ||
Others | emd_42820_half_map_1.map.gz emd_42820_half_map_2.map.gz | 475.7 MB 475.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42820 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42820 | HTTPS FTP |
-Validation report
Summary document | emd_42820_validation.pdf.gz | 689.3 KB | Display | EMDB validaton report |
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Full document | emd_42820_full_validation.pdf.gz | 688.8 KB | Display | |
Data in XML | emd_42820_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | emd_42820_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42820 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42820 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42820.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 RNA SL5-6 domains with SL5b extended. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.741 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_42820_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map of the SARS-CoV-2 RNA SL5-6 domains with SL5b extended.
File | emd_42820_half_map_1.map | ||||||||||||
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Annotation | Half map of the SARS-CoV-2 RNA SL5-6 domains with SL5b extended. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of the SARS-CoV-2 RNA SL5-6 domains with SL5b extended.
File | emd_42820_half_map_2.map | ||||||||||||
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Annotation | Half map of the SARS-CoV-2 RNA SL5-6 domains with SL5b extended. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5b extended
Entire | Name: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5b extended |
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Components |
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-Supramolecule #1: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5b extended
Supramolecule | Name: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5b extended type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 65.7 KDa |
-Macromolecule #1: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5b extended
Macromolecule | Name: SARS-CoV-2 5' proximal stem-loop 5 and 6 with SL5b extended type: rna / ID: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Sequence | String: UGUCGUUGAC AGGACACGAG UAACUCGUCU AUCUUCUGCA GGCUGCUUAC GGUUUCGUCC GUGUUGCAGC CGAUCAUCAG CACAUCUAGC UGGGUUUCGU CCCAGCGGGU GUGACCGAAA GGUAAGAUGG AGAGCCUUGU CCCUGGUUUC AACGAGAAAA CACACGUCCA ...String: UGUCGUUGAC AGGACACGAG UAACUCGUCU AUCUUCUGCA GGCUGCUUAC GGUUUCGUCC GUGUUGCAGC CGAUCAUCAG CACAUCUAGC UGGGUUUCGU CCCAGCGGGU GUGACCGAAA GGUAAGAUGG AGAGCCUUGU CCCUGGUUUC AACGAGAAAA CACACGUCCA ACUCAGUUUG CCUGUUUUAC AGGUUCGCGA CGUG GENBANK: GENBANK: NC_045512.2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.31 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: 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 | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11496 / Average exposure time: 4.66 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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