+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42818 | ||||||||||||||||||||||||||||||||||||
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Title | SARS-CoV-2 5' proximal stem-loop 5 | ||||||||||||||||||||||||||||||||||||
Map data | SARS-CoV-1 RNA SL5 domain. | ||||||||||||||||||||||||||||||||||||
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: 4.7 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, China, 11 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42818.map.gz | 90.8 MB | EMDB map data format | |
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Header (meta data) | emd-42818-v30.xml emd-42818.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42818_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_42818.png | 45.7 KB | ||
Masks | emd_42818_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-42818.cif.gz | 5.9 KB | ||
Others | emd_42818_half_map_1.map.gz emd_42818_half_map_2.map.gz | 165.4 MB 165.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42818 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42818 | HTTPS FTP |
-Related structure data
Related structure data | 8uysMC 8uyeC 8uygC 8uyjC 8uykC 8uylC 8uymC 8uypC C: citing same article (ref.) M: atomic model generated by this map |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42818.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | SARS-CoV-1 RNA SL5 domain. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_42818_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 domain.
File | emd_42818_half_map_1.map | ||||||||||||
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Annotation | Half map of the SARS-CoV-2 RNA SL5 domain. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of the SARS-CoV-2 RNA SL5 domain.
File | emd_42818_half_map_2.map | ||||||||||||
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Annotation | Half map of the SARS-CoV-2 RNA SL5 domain. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 5' proximal stem-loop 5
Entire | Name: SARS-CoV-2 5' proximal stem-loop 5 |
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Components |
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-Supramolecule #1: SARS-CoV-2 5' proximal stem-loop 5
Supramolecule | Name: SARS-CoV-2 5' proximal stem-loop 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 40.03 KDa |
-Macromolecule #1: SARS-CoV-2 RNA SL5 domain.
Macromolecule | Name: SARS-CoV-2 RNA SL5 domain. / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 39.807484 KDa |
Sequence | String: GGACACGAGU AACUCGUCUA UCUUCUGCAG GCUGCUUACG GUUUCGUCCG UGUUGCAGCC GAUCAUCAGC ACAUCUAGGU UUCGUCCGG GUGUGACCGA AAGGUAAGAU GGAGAGCCUU GUCCC 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 | 1.20 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 Details: 1 of the 4 grids was Quantifoil R 2/1 grids (Cu, 200 mesh) | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | 1 of the 4 grids was at 0.80 mg/mL |
-Electron microscopy
Microscope | TFS KRIOS |
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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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: 26164 / Average exposure time: 4.88 sec. / Average electron dose: 50.0 e/Å2 Details: For collections had exposure times of 6.00s, 3.84s, 4.13s, 5.56s. Four collection had 11,815, 4,217, 4,592 5,540 micrographs. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-8uys: |