[English] 日本語
Yorodumi- EMDB-36159: Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36159 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GpppAmU | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | nonstructural protein / Chikungunya virus / RNA cap / replication / 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 / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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: 2.41 Å | |||||||||
Authors | Zhang K / Law MCY / Nguyen TM / Tan YB / Wirawan M / Law YS / Luo DH | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: J Biol Chem / Year: 2023 Title: Chikungunya virus nonstructural protein 1 is a versatile RNA capping and decapping enzyme. Authors: Michelle Cheok Yien Law / Kuo Zhang / Yaw Bia Tan / Trinh Mai Nguyen / Dahai Luo / Abstract: Chikungunya virus (CHIKV) nonstructural protein 1 (nsP1) contains both the N7-guanine methyltransferase and guanylyltransferase activities and catalyzes the 5' end cap formation of viral RNAs. To ...Chikungunya virus (CHIKV) nonstructural protein 1 (nsP1) contains both the N7-guanine methyltransferase and guanylyltransferase activities and catalyzes the 5' end cap formation of viral RNAs. To further understand its catalytic activity and role in virus-host interaction, we demonstrate that purified recombinant CHIKV nsP1 can reverse the guanylyl transfer reaction and remove the mGMP from a variety of capped RNA substrates including host mRNAs. We then provide the structural basis of this function with a high-resolution cryo-EM structure of nsP1 in complex with the unconventional cap-1 substrate RNA mGpppAU. We show that the 5'ppRNA species generated by decapping can trigger retinoic acid-inducible gene I-mediated interferon response. We further demonstrate that the decapping activity is conserved among the alphaviral nsP1s. To our knowledge, this is a new mechanism through which alphaviruses activate the antiviral immune response. This decapping activity could promote cellular mRNA degradation and facilitate viral gene expression, which is functionally analogous to the cap-snatching mechanism by influenza virus. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_36159.map.gz | 208.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-36159-v30.xml emd-36159.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
Images | emd_36159.png | 235.8 KB | ||
Filedesc metadata | emd-36159.cif.gz | 5.8 KB | ||
Others | emd_36159_half_map_1.map.gz emd_36159_half_map_2.map.gz | 323.3 MB 340.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36159 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36159 | HTTPS FTP |
-Related structure data
Related structure data | 8jceMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_36159.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_36159_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_36159_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Nonstructural Protein 1
Entire | Name: Nonstructural Protein 1 |
---|---|
Components |
|
-Supramolecule #1: Nonstructural Protein 1
Supramolecule | Name: Nonstructural Protein 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
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 |
---|---|
Source (natural) | Organism: Chikungunya virus strain S27-African prototype |
Molecular weight | Theoretical: 61.989477 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDPVYVDIDA DSAFLKALQR AYPMFEVEPR QVTPNDAANA RAFSHLAIKL IEQEIDPDST ILDIGSAPAR RMMSDRKYHC VCPMRSAED PERLANYARK LASAAGKVLD RNISGKIGDL QAVMAVPDTE TPTFCLHTDV SCRQRADVAI YQDVYAVHAP T SLYHQAIK ...String: MDPVYVDIDA DSAFLKALQR AYPMFEVEPR QVTPNDAANA 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 |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: S-ADENOSYL-L-HOMOCYSTEINE
Macromolecule | Name: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 3 / Number of copies: 12 / Formula: SAH |
---|---|
Molecular weight | Theoretical: 384.411 Da |
Chemical component information | ChemComp-SAH: |
-Macromolecule #4: [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[...
Macromolecule | Name: [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy- ...Name: [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate type: ligand / ID: 4 / Number of copies: 12 / Formula: YG4 |
---|---|
Molecular weight | Theoretical: 1.110657 KDa |
Chemical component information | ChemComp-YG4: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 588 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70128 |