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Yorodumi- EMDB-32914: Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32914 | |||||||||
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Title | Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with inhibitor FHA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nonstructural Protein / Chikungunya Virus / RNA cap / inhibitor / VIRAL PROTEIN | |||||||||
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: 2.62 Å | |||||||||
Authors | Zhang K / Law MCY | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Rep / Year: 2022 Title: Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1. Authors: Kuo Zhang / Michelle Cheok Yien Law / Trinh Mai Nguyen / Yaw Bia Tan / Melissa Wirawan / Yee-Song Law / Lak Shin Jeong / Dahai Luo / Abstract: Many viruses encode RNA-modifying enzymes to edit the 5' end of viral RNA to mimic the cellular mRNA for effective protein translation, genome replication, and evasion of the host defense mechanisms. ...Many viruses encode RNA-modifying enzymes to edit the 5' end of viral RNA to mimic the cellular mRNA for effective protein translation, genome replication, and evasion of the host defense mechanisms. Alphavirus nsP1 synthesizes the 5' end Cap-0 structure of viral RNAs. However, the molecular basis of the capping process remains unclear. We determine high-resolution cryoelectron microscopy (cryo-EM) structures of Chikungunya virus nsP1 in complex with m7GTP/SAH, covalently attached m7GMP, and Cap-0 viral RNA. These structures reveal details of viral-RNA-capping reactions and uncover a sequence-specific virus RNA-recognition pattern that, in turn, regulates viral-RNA-capping efficiency to ensure optimal genome replication and subgenomic RNA transcription. This sequence-specific enzyme-RNA pairing is conserved across all alphaviruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32914.map.gz | 398.1 MB | EMDB map data format | |
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Header (meta data) | emd-32914-v30.xml emd-32914.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_32914.png | 85.5 KB | ||
Filedesc metadata | emd-32914.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32914 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32914 | HTTPS FTP |
-Validation report
Summary document | emd_32914_validation.pdf.gz | 544.4 KB | Display | EMDB validaton report |
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Full document | emd_32914_full_validation.pdf.gz | 544 KB | Display | |
Data in XML | emd_32914_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_32914_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32914 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32914 | HTTPS FTP |
-Related structure data
Related structure data | 7x01MC 7fggC 7fghC 7fgiC 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_32914.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Nonstructural Protein 1
Entire | Name: Nonstructural Protein 1 |
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Components |
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-Supramolecule #1: Nonstructural Protein 1
Supramolecule | Name: Nonstructural Protein 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Chikungunya virus strain S27-African prototype |
-Macromolecule #1: mRNA-capping enzyme nsP1
Macromolecule | Name: mRNA-capping enzyme nsP1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO EC number: Transferases; Transferring one-carbon groups; Methyltransferases |
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Source (natural) | Organism: Chikungunya virus strain S27-African prototype |
Molecular weight | Theoretical: 62.056539 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 AAGGGGSWSH PQFEKMDYKD HDGDYKDHDI DYKDDDDK UniProtKB: Polyprotein P1234 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: (1R,2S,3S,4R,5R)-3-(6-aminopurin-9-yl)-4-fluoranyl-5-(2-hydroxyet...
Macromolecule | Name: (1R,2S,3S,4R,5R)-3-(6-aminopurin-9-yl)-4-fluoranyl-5-(2-hydroxyethyl)cyclopentane-1,2-diol type: ligand / ID: 3 / Number of copies: 12 / Formula: 7XQ |
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Molecular weight | Theoretical: 297.286 Da |
Chemical component information | ChemComp-7XQ: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76791 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |