[English] 日本語
Yorodumi- PDB-5yku: The crystal structure of Macrobrachium rosenbergii nodavirus P-do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yku | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Zn ions | ||||||
Components | Capsid protein | ||||||
Keywords | VIRAL PROTEIN / Protrusion domain of viral capsid protein | ||||||
Function / homology | Viral coat protein subunit / metal ion binding / Capsid protein alpha Function and homology information | ||||||
Biological species | Macrobrachium rosenbergii nodavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Chen, N.C. / Yoshimura, M. / Lin, C.C. / Guan, H.H. / Chuankhayan, P. / Chen, C.J. | ||||||
Funding support | Taiwan, 1items
| ||||||
Citation | Journal: Commun Biol / Year: 2019 Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi ...Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi Nakagawa / Sunney I Chan / Chun-Jung Chen / Abstract: Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity ...Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of = 3 and = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls = 3 and = 1 assemblies. Increasing the /-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yku.cif.gz | 43 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yku.ent.gz | 31.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yku_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5yku_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 5yku_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 5yku_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5yku ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5yku | HTTPS FTP |
-Related structure data
Related structure data | 6999C 9576C 5ykvC 5ykxC 5ykzC 5yl0C 5yl1C 6ab5C 6ab6C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13880.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrobrachium rosenbergii nodavirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XNL3 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.33 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 10% PEG8000, MES pH 6.5, 0.2 M Zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→30 Å / Num. obs: 29388 / % possible obs: 99.2 % / Redundancy: 9.6 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.075 / Rsym value: 0.07 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.39→1.44 Å / Redundancy: 9.9 % / CC1/2: 0.964 / Rpim(I) all: 0.113 / Rrim(I) all: 0.356 / Rsym value: 0.337 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→23.87 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.582 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.247 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.39→23.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|