[English] 日本語
![](img/lk-miru.gif)
- EMDB-31580: Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 wi... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GTP | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() host cell filopodium / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zhang K / Law MCY | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 398.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 11 KB 11 KB | Display Display | ![]() |
Images | ![]() | 68.6 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fggMC ![]() 7fghC ![]() 7fgiC ![]() 7x01C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
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: ![]() ![]() |
-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: ![]() |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 62.056539 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 |
---|---|
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: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 12 / Formula: MGP |
---|---|
Molecular weight | Theoretical: 538.215 Da |
Chemical component information | ![]() ChemComp-MGP: |
-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: 1764 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
---|---|
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 244484 |