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Yorodumi- EMDB-15555: CryoEM structure of the Chikungunya virus nsP1 capping pores in c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15555 | |||||||||
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Title | CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with SAM | |||||||||
Map data | CHIKV nsP1 capping pores in complex with SAM ligand | |||||||||
Sample |
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Function / homology | Function and homology information host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Chikungunya virus strain S27-African prototype | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Jones R / Hons M / Reguera J | |||||||||
Funding support | France, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structural basis and dynamics of Chikungunya alphavirus RNA capping by nsP1 capping pores. Authors: Rhian Jones / Michael Hons / Nadia Rabah / Noelia Zamarreño / Rocío Arranz / Juan Reguera / Abstract: Alphaviruses are emerging positive-stranded RNA viruses which replicate and transcribe their genomes in membranous organelles formed in the cell cytoplasm. The nonstructural protein 1 (nsP1) is ...Alphaviruses are emerging positive-stranded RNA viruses which replicate and transcribe their genomes in membranous organelles formed in the cell cytoplasm. The nonstructural protein 1 (nsP1) is responsible for viral RNA capping and gates the replication organelles by assembling into monotopic membrane-associated dodecameric pores. The capping pathway is unique to Alphaviruses; beginning with the N methylation of a guanosine triphosphate (GTP) molecule, followed by the covalent linkage of an mGMP group to a conserved histidine in nsP1 and the transfer of this cap structure to a diphosphate RNA. Here, we provide structural snapshots of different stages of the reaction pathway showing how nsP1 pores recognize the substrates of the methyl-transfer reaction, GTP and S-adenosyl methionine (SAM), how the enzyme reaches a metastable postmethylation state with SAH and mGTP in the active site, and the subsequent covalent transfer of mGMP to nsP1 triggered by the presence of RNA and postdecapping reaction conformational changes inducing the opening of the pore. In addition, we biochemically characterize the capping reaction, demonstrating specificity for the RNA substrate and the reversibility of the cap transfer resulting in decapping activity and the release of reaction intermediates. Our data identify the molecular determinants allowing each pathway transition, providing an explanation for the need for the SAM methyl donor all along the pathway and clues about the conformational rearrangements associated to the enzymatic activity of nsP1. Together, our results set ground for the structural and functional understanding of alphavirus RNA-capping and the design of antivirals. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15555.map.gz | 25.6 MB | EMDB map data format | |
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Header (meta data) | emd-15555-v30.xml emd-15555.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15555_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_15555.png | 109.8 KB | ||
Others | emd_15555_half_map_1.map.gz emd_15555_half_map_2.map.gz | 75.9 MB 75.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15555 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15555 | HTTPS FTP |
-Related structure data
Related structure data | 8aoxMC 8aovC 8aowC 8apxC 8axvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15555.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CHIKV nsP1 capping pores in complex with SAM ligand | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.827 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: halfmap1
File | emd_15555_half_map_1.map | ||||||||||||
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Annotation | halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap2
File | emd_15555_half_map_2.map | ||||||||||||
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Annotation | halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CHIKV nsP1 capping pores in complex with S-adenosyl methionine (S...
Entire | Name: CHIKV nsP1 capping pores in complex with S-adenosyl methionine (SAM) ligand. |
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Components |
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-Supramolecule #1: CHIKV nsP1 capping pores in complex with S-adenosyl methionine (S...
Supramolecule | Name: CHIKV nsP1 capping pores in complex with S-adenosyl methionine (SAM) ligand. type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Chikungunya virus strain S27-African prototype |
Molecular weight | Theoretical: 1.2 MDa |
-Macromolecule #1: mRNA-capping enzyme nsP1
Macromolecule | Name: mRNA-capping enzyme nsP1 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO EC number: Transferases; Transferring one-carbon groups; Methyltransferases |
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Source (natural) | Organism: Chikungunya virus strain S27-African prototype / Strain: S27-African prototype |
Molecular weight | Theoretical: 59.975422 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: MDPVYVDIDA DSAFLKALQR AYPMFEVEPR QVTPNDHANA RAFSHLAIKL IEQEIDPDST ILDIGSAPAR RMMSDRKYHC VCPMRSAED PERLANYARK LASAAGKVLD RNISGKIGDL QAVMAVPDTE TPTFCLHTDV SCRQRADVAI YQDVYAVHAP T SLYHQAIK ...String: MDPVYVDIDA DSAFLKALQR AYPMFEVEPR QVTPNDHANA RAFSHLAIKL IEQEIDPDST ILDIGSAPAR RMMSDRKYHC VCPMRSAED PERLANYARK LASAAGKVLD RNISGKIGDL QAVMAVPDTE TPTFCLHTDV SCRQRADVAI YQDVYAVHAP T SLYHQAIK GVRLAYWVGF DTTPFMYNAM AGAYPSYSTN WADEQVLKAK NIGLCSTDLT EGRRGKLSIM RGKKLEPCDR VL FSVGSTL YPESRKLLKS WHLPSVFHLK GKLSFTCRCD TVVSCEGYVV KRITMSPGLY GKTTGYAVTH HADGFLMCKT TDT VDGERV SFSVCTYVPA TICDQMTGIL ATEVTPEDAQ KLLVGLNQRI VVNGRTQRNT NTMKNYMIPV VAQAFSKWAK ECRK DMEDE KLLGVRERTL TCCCLWAFKK QKTHTVYKRP DTQSIQKVQA EFDSFVVPSL WSSGLSIPLR TRIKWLLSKV PKTDL TPYS GDAQEARDAE KEAEEEREAE LTLEALPPLQ AAQEDVQVEI DVEQLEDRAG A |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: S-ADENOSYLMETHIONINE
Macromolecule | Name: S-ADENOSYLMETHIONINE / type: ligand / ID: 3 / Number of copies: 24 / Formula: SAM |
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Molecular weight | Theoretical: 398.437 Da |
Chemical component information | ChemComp-SAM: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 4848 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Specimen was incubated with 0.5mM SAM |
-Electron microscopy
Microscope | FEI TITAN 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4500 / Average exposure time: 4.0 sec. / Average electron dose: 42.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |