[English] 日本語
Yorodumi- PDB-8kdb: Cryo-EM structure of the human parainfluenza virus hPIV3 L-P poly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8kdb | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human parainfluenza virus hPIV3 L-P polymerase in dimeric form | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN / dimeric polymerase / parainfluenza virus / L-P polymerase / cryo-EM structure / non-segmented negative-strand RNA virus / L-L dimerization / RNA replication / RdRp active site | ||||||
Function / homology | Function and homology information GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity ...GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / DNA-templated transcription / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Human respirovirus 3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Xie, J. / Wang, L. / Zhai, G. / Wu, D. / Lin, Z. / Wang, M. / Yan, X. / Gao, L. / Huang, X. / Fearns, R. / Chen, S. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for dimerization of a paramyxovirus polymerase complex. Authors: Jin Xie / Mohamed Ouizougun-Oubari / Li Wang / Guanglei Zhai / Daitze Wu / Zhaohu Lin / Manfu Wang / Barbara Ludeke / Xiaodong Yan / Tobias Nilsson / Lu Gao / Xinyi Huang / Rachel Fearns / Shuai Chen / Abstract: The transcription and replication processes of non-segmented, negative-strand RNA viruses (nsNSVs) are catalyzed by a multi-functional polymerase complex composed of the large protein (L) and a ...The transcription and replication processes of non-segmented, negative-strand RNA viruses (nsNSVs) are catalyzed by a multi-functional polymerase complex composed of the large protein (L) and a cofactor protein, such as phosphoprotein (P). Previous studies have shown that the nsNSV polymerase can adopt a dimeric form, however, the structure of the dimer and its function are poorly understood. Here we determine a 2.7 Å cryo-EM structure of human parainfluenza virus type 3 (hPIV3) L-P complex with the connector domain (CD') of a second L built, while reconstruction of the rest of the second L-P obtains a low-resolution map of the ring-like L core region. This study reveals detailed atomic features of nsNSV polymerase active site and distinct conformation of hPIV3 L with a unique β-strand latch. Furthermore, we report the structural basis of L-L dimerization, with CD' located at the putative template entry of the adjoining L. Disruption of the L-L interface causes a defect in RNA replication that can be overcome by complementation, demonstrating that L dimerization is necessary for hPIV3 genome replication. These findings provide further insight into how nsNSV polymerases perform their functions, and suggest a new avenue for rational drug design. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8kdb.cif.gz | 545 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8kdb.ent.gz | 396.2 KB | Display | PDB format |
PDBx/mmJSON format | 8kdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/8kdb ftp://data.pdbj.org/pub/pdb/validation_reports/kd/8kdb | HTTPS FTP |
---|
-Related structure data
Related structure data | 37130MC 8kdcC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 260103.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NP_067153.2 / Source: (gene. exp.) Human respirovirus 3 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O89238 #2: Protein | Mass: 68471.312 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: NP_067149.1 / Source: (gene. exp.) Human respirovirus 3 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O89234 #3: Chemical | ChemComp-MG / | #4: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human parainfluenza virus hPIV3 L-P polymerase in dimeric form Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Human respirovirus 3 |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf21 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Image processing |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction |
| |||||||||||||||||||||||||||||||||||
3D reconstruction |
| |||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 2.7 Å |