[English] 日本語
Yorodumi
- PDB-7xpn: Structure of the Spring Viraemia of Carp Virus Nucleoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xpn
TitleStructure of the Spring Viraemia of Carp Virus Nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SVCV / RNP / VIRUS
Biological speciesSprivirus cyprinus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.98 Å
AuthorsWang, Z.X. / Liu, B. / Zhang, Y.A. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725026, 31770948, 31570875 China
CitationJournal: J Virol / Year: 2023
Title: Structure of the Spring Viraemia of Carp Virus Ribonucleoprotein Complex Reveals Its Assembly Mechanism and Application in Antiviral Drug Screening.
Authors: Zhao-Xi Wang / Bing Liu / Tian Yang / Daqi Yu / Chu Zhang / Liming Zheng / Jin Xie / Bin Liu / Mengxi Liu / Hailin Peng / Luhua Lai / Qi Ouyang / Songying Ouyang / Yong-An Zhang /
Abstract: Spring viremia of carp virus (SVCV) is a highly pathogenic infecting the common carp, yet neither a vaccine nor effective therapies are available to treat spring viremia of carp (SVC). Like all ...Spring viremia of carp virus (SVCV) is a highly pathogenic infecting the common carp, yet neither a vaccine nor effective therapies are available to treat spring viremia of carp (SVC). Like all negative-sense viruses, SVCV contains an RNA genome that is encapsidated by the nucleoprotein (N) in the form of a ribonucleoprotein (RNP) complex, which serves as the template for viral replication and transcription. Here, the three-dimensional (3D) structure of SVCV RNP was resolved through cryo-electron microscopy (cryo-EM) at a resolution of 3.7 Å. RNP assembly was stabilized by N and C loops; RNA was wrapped in the groove between the N and C lobes with 9 nt nucleotide per protomer. Combined with mutational analysis, our results elucidated the mechanism of RNP formation. The RNA binding groove of SVCV N was used as a target for drug virtual screening, and it was found suramin had a good antiviral effect. This study provided insights into RNP assembly, and anti-SVCV drug screening was performed on the basis of this structure, providing a theoretical basis and efficient drug screening method for the prevention and treatment of SVC. Aquaculture accounts for about 70% of global aquatic products, and viral diseases severely harm the development of aquaculture industry. Spring viremia of carp virus (SVCV) is the pathogen causing highly contagious spring viremia of carp (SVC) disease in cyprinids, especially common carp (), yet neither a vaccine nor effective therapies are available to treat this disease. In this study, we have elucidated the mechanism of SVCV ribonucleoprotein complex (RNP) formation by resolving the 3D structure of SVCV RNP and screened antiviral drugs based on the structure. It is found that suramin could competitively bind to the RNA binding groove and has good antiviral effects both and . Our study provides a template for rational drug discovery efforts to treat and prevent SVCV infections.
History
DepositionMay 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
I: Nucleoprotein
K: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
D: Nucleoprotein
J: Nucleoprotein
L: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)564,62112
Polymers564,62112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.250, 298.700, 332.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 2 - 418 / Label seq-ID: 2 - 418

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BF
d_3CG
d_4DJ
d_5EB
d_6FC
d_7GH
d_8HI
d_9ID
d_10JK
d_11KE
d_12LL

NCS oper:
IDCodeMatrixVector
1given(0.0395965593036, 0.977375980321, 0.207769838003), (-0.9780623816, -0.00464746104146, 0.20826036302), (0.204514278696, -0.211458256396, 0.955750655564)-74.8022681718, 111.526193348, 16.4988259051
2given(-0.795424720936, 0.477557374966, 0.373146709672), (-0.471209619096, -0.874523323209, 0.114762589878), (0.381131221753, -0.0845453179037, 0.92064709907)-14.0122209613, 184.604760806, 2.76843431422
3given(-0.439433685474, -0.840730703821, 0.31633829949), (0.84451287401, -0.506671129459, -0.173442705825), (0.306098091634, 0.190935199022, 0.932656264694)105.208815059, 126.613799031, -22.4109135721
4given(0.50994699088, 0.853099397323, 0.110342579174), (-0.854732274123, 0.488068481691, 0.176697189428), (0.0968855307262, -0.184419563676, 0.978060641509)-70.8892182928, 62.5234572003, 15.7365303752
5given(0.884661725347, -0.466037543118, 0.0135144408351), (0.464524595949, 0.878569373036, -0.111052944677), (0.039881467682, 0.104522079812, 0.993722598801)46.7273374459, 3.53503869097, -10.760332185
6given(-0.915250303957, -0.0208546633221, 0.402345577985), (0.0266878454175, -0.999604223261, 0.00889695151326), (0.402000796036, 0.0188806741665, 0.915444635207)34.6032301209, 187.753132174, -7.36858248126
7given(-0.442915264065, 0.840323957087, 0.312540742951), (-0.84091625353, -0.510265990191, 0.180245593018), (0.310943601649, -0.18298706621, 0.932646669534)-53.8306090408, 156.441602074, 11.9162158993
8given(0.868568748468, 0.494936938365, 0.0250151199667), (-0.494713863898, 0.863001605751, 0.102403229136), (0.0290950520078, -0.101319571224, 0.994428389798)-43.9636411252, 21.2677933821, 9.37668366339
9given(-0.773201607548, -0.505382507774, 0.383076748083), (0.50597156871, -0.855791197206, -0.107769190591), (0.382298372666, 0.110498631755, 0.917408309662)78.0681184215, 165.970983734, -16.3776368443
10given(0.531882514901, -0.840709090049, 0.10153431071), (0.840241803639, 0.509030792116, -0.186765532408), (0.105331390195, 0.184650693436, 0.977143500031)87.6676101576, 31.693230596, -19.1563402471
11given(0.0699037553166, -0.974651341109, 0.21252818229), (0.9747417023, 0.021435574054, -0.222304138426), (0.212113363061, 0.222699976291, 0.951531734505)108.673827895, 75.5319802046, -23.9521254973

-
Components

#1: Protein
Nucleoprotein


Mass: 47051.723 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sprivirus cyprinus
Production host: Insect expression vector pBlueBacmsGCB1His (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 289.15 K / Method: liquid diffusion / pH: 5.8
Details: 0.2 M Ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.8, 21% v/v Polyethylene glycol 400

-
Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.98→75.26 Å / Num. obs: 74437 / % possible obs: 99.86 % / Redundancy: 13.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.0566 / Rpim(I) all: 0.0566 / Rrim(I) all: 0.08004 / Net I/σ(I): 11.54
Reflection shellResolution: 3.98→4.122 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.3418 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 7391 / CC1/2: 0.802 / CC star: 0.943 / Rpim(I) all: 0.3418 / Rrim(I) all: 0.4834 / % possible all: 99.88

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gic

2gic


Resolution: 3.98→72.86 Å / SU ML: 0.5921 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2843 3813 2.65 %
Rwork0.2547 139821 -
obs0.2555 74388 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.98→72.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39588 0 0 0 39588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00340500
X-RAY DIFFRACTIONf_angle_d0.854900
X-RAY DIFFRACTIONf_chiral_restr0.04926024
X-RAY DIFFRACTIONf_plane_restr0.00526996
X-RAY DIFFRACTIONf_dihedral_angle_d5.09545448
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.25309900806
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.1055517724
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.25717944398
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.25153537881
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.49410213811
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.15297526474
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS1.32874052707
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS1.15798546399
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS1.23758820328
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS1.18768756929
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS1.19142518588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.98-4.030.40271410.35325249X-RAY DIFFRACTION99.83
4.03-4.080.38221460.35165143X-RAY DIFFRACTION99.91
4.08-4.140.32681460.3185162X-RAY DIFFRACTION99.92
4.14-4.20.34241370.31225203X-RAY DIFFRACTION100
4.2-4.260.33031420.29615174X-RAY DIFFRACTION99.92
4.26-4.330.30671290.29495216X-RAY DIFFRACTION99.87
4.33-4.40.29421610.28335125X-RAY DIFFRACTION99.96
4.4-4.470.34271320.29235200X-RAY DIFFRACTION99.96
4.47-4.560.31211580.28525194X-RAY DIFFRACTION99.93
4.56-4.640.28261260.28395157X-RAY DIFFRACTION99.91
4.64-4.740.34711460.29725173X-RAY DIFFRACTION99.94
4.74-4.840.33091480.28335168X-RAY DIFFRACTION99.96
4.84-4.950.32531450.27785214X-RAY DIFFRACTION99.94
4.95-5.080.33911390.27025162X-RAY DIFFRACTION99.96
5.08-5.210.30641350.26535211X-RAY DIFFRACTION99.96
5.21-5.370.25151460.2685165X-RAY DIFFRACTION99.98
5.37-5.540.35211360.27495170X-RAY DIFFRACTION99.96
5.54-5.740.2891350.28375187X-RAY DIFFRACTION99.78
5.74-5.970.31981400.35174X-RAY DIFFRACTION100
5.97-6.240.31551480.27745186X-RAY DIFFRACTION100
6.24-6.570.32921350.26195184X-RAY DIFFRACTION99.85
6.57-6.980.31051490.25475155X-RAY DIFFRACTION99.96
6.98-7.520.25271410.22785213X-RAY DIFFRACTION99.96
7.52-8.270.22411500.20615159X-RAY DIFFRACTION100
8.28-9.470.20161460.17975152X-RAY DIFFRACTION99.98
9.47-11.920.19661370.16685145X-RAY DIFFRACTION99.29
11.92-72.860.3031190.26895180X-RAY DIFFRACTION99.05

+
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://pdbjlvh1.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