[English] 日本語
Yorodumi
- PDB-5ykx: The crystal structure of Macrobrachium rosenbergii nodavirus P-do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ykx
TitleThe crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Cd ion
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / viral capsid protein
Function / homologyViral coat protein subunit / : / Capsid protein alpha
Function and homology information
Biological speciesMacrobrachium rosenbergii nodavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, N.C. / Yoshimura, M. / Lin, C.C. / Guan, H.H. / Chuankhayan, P. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology105-2311-B-213-001-MY3 Taiwan
CitationJournal: 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
DepositionOct 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4327
Polymers27,7612
Non-polymers6725
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-39 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.175, 134.175, 134.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-201-

CD

21B-201-

CD

31A-334-

HOH

41A-464-

HOH

51B-305-

HOH

61B-414-

HOH

-
Components

#1: Protein Capsid protein / Capsid


Mass: 13880.379 Da / Num. of mol.: 2
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 ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.0M Sodium acetate trihydrate, 0.1M Sodium HEPES 7.5, 0.05M Cadmium sulfate 8/3-hydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 28636 / % possible obs: 99.9 % / Redundancy: 20 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.115 / Rsym value: 0.112 / Net I/σ(I): 41.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 19 % / CC1/2: 0.953 / Rpim(I) all: 0.191 / Rrim(I) all: 0.853 / Rsym value: 0.83 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.3 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.354 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19478 1439 5 %RANDOM
Rwork0.15587 ---
obs0.15781 27072 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 23 308 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021938
X-RAY DIFFRACTIONr_bond_other_d0.0010.021799
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.9652645
X-RAY DIFFRACTIONr_angle_other_deg0.9934152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4075239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84625.52985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40815303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.046156
X-RAY DIFFRACTIONr_chiral_restr0.1420.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7622.469962
X-RAY DIFFRACTIONr_mcbond_other2.7512.467961
X-RAY DIFFRACTIONr_mcangle_it3.6983.6791199
X-RAY DIFFRACTIONr_mcangle_other3.73.681200
X-RAY DIFFRACTIONr_scbond_it4.862.926976
X-RAY DIFFRACTIONr_scbond_other4.6322.918972
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0074.2111441
X-RAY DIFFRACTIONr_long_range_B_refined24.95926.2312645
X-RAY DIFFRACTIONr_long_range_B_other24.41624.5222454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 102 -
Rwork0.161 1938 -
obs--99.37 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more