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- PDB-8hif: One asymmetric unit of Singapore grouper iridovirus capsid -

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Basic information

Entry
Database: PDB / ID: 8hif
TitleOne asymmetric unit of Singapore grouper iridovirus capsid
Components
  • Major capsid protein
  • Penton protein (VP14)
  • VP137
  • VP139
  • VP38
  • VP59
  • VP88
KeywordsVIRAL PROTEIN / Singapore grouper iridovirus / capsid proteins
Function / homology
Function and homology information


viral capsid / structural molecule activity / membrane
Similarity search - Function
Protein of unknown function DUF5850 / Family of unknown function (DUF5850) / Virion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Major capsid protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesSingapore grouper iridovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhao, Z.N. / Liu, C.C. / Zhu, D.J. / Qi, J.X. / Zhang, X.Z. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2023
Title: Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly.
Authors: Zhennan Zhao / Youhua Huang / Congcong Liu / Dongjie Zhu / Shuaixin Gao / Sheng Liu / Ruchao Peng / Ya Zhang / Xiaohong Huang / Jianxun Qi / Catherine C L Wong / Xinzheng Zhang / Peiyi Wang ...Authors: Zhennan Zhao / Youhua Huang / Congcong Liu / Dongjie Zhu / Shuaixin Gao / Sheng Liu / Ruchao Peng / Ya Zhang / Xiaohong Huang / Jianxun Qi / Catherine C L Wong / Xinzheng Zhang / Peiyi Wang / Qiwei Qin / George F Gao /
Abstract: Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and ...Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and significantly threatens global biodiversity. In recent years, high morbidity and mortality in aquatic animals have been caused by iridovirid infections worldwide. Effective control and prevention strategies are urgently needed. Here, we present a near-atomic architecture of the SGIV capsid and identify eight types of capsid proteins. The viral inner membrane-integrated anchor protein colocalizes with the endoplasmic reticulum (ER), supporting the hypothesis that the biogenesis of the inner membrane is associated with the ER. Additionally, immunofluorescence assays indicate minor capsid proteins (mCPs) could form various building blocks with major capsid proteins (MCPs) before the formation of a viral factory (VF). These results expand our understanding of the capsid assembly of NCVs and provide more targets for vaccine and drug design to fight iridovirid infections.
History
DepositionNov 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Major capsid protein
A2: Major capsid protein
A3: Major capsid protein
B1: Major capsid protein
B2: Major capsid protein
B3: Major capsid protein
C1: Major capsid protein
C2: Major capsid protein
C3: Major capsid protein
D1: Major capsid protein
D2: Major capsid protein
D3: Major capsid protein
E1: Major capsid protein
E2: Major capsid protein
E3: Major capsid protein
F1: Major capsid protein
F2: Major capsid protein
F3: Major capsid protein
G1: Major capsid protein
G2: Major capsid protein
G3: Major capsid protein
H1: Major capsid protein
H2: Major capsid protein
H3: Major capsid protein
I1: Major capsid protein
I2: Major capsid protein
I3: Major capsid protein
J1: Major capsid protein
J3: Major capsid protein
K1: Major capsid protein
K2: Major capsid protein
K3: Major capsid protein
L1: Major capsid protein
L2: Major capsid protein
L3: Major capsid protein
M1: Major capsid protein
M2: Major capsid protein
M3: Major capsid protein
N1: Major capsid protein
N2: Major capsid protein
N3: Major capsid protein
O1: Major capsid protein
O2: Major capsid protein
O3: Major capsid protein
P1: Major capsid protein
P2: Major capsid protein
P3: Major capsid protein
Q1: Major capsid protein
Q2: Major capsid protein
Q3: Major capsid protein
R1: Major capsid protein
R2: Major capsid protein
R3: Major capsid protein
S1: Major capsid protein
S2: Major capsid protein
S3: Major capsid protein
T1: Major capsid protein
T2: Major capsid protein
T3: Major capsid protein
U1: Major capsid protein
U2: Major capsid protein
U3: Major capsid protein
V1: Major capsid protein
V2: Major capsid protein
V3: Major capsid protein
W1: Major capsid protein
W2: Major capsid protein
W3: Major capsid protein
X1: Major capsid protein
X2: Major capsid protein
X3: Major capsid protein
Y1: Major capsid protein
Y2: Major capsid protein
Y3: Major capsid protein
Z1: Major capsid protein
Z2: Major capsid protein
Z3: Major capsid protein
a1: Major capsid protein
a2: Major capsid protein
a3: Major capsid protein
b1: Major capsid protein
b2: Major capsid protein
b3: Major capsid protein
d1: Major capsid protein
d2: Major capsid protein
d3: Major capsid protein
e1: Major capsid protein
e2: Major capsid protein
e3: Major capsid protein
f1: Major capsid protein
f2: Major capsid protein
f3: Major capsid protein
g1: Major capsid protein
g2: Major capsid protein
g3: Major capsid protein
h1: Major capsid protein
h2: Major capsid protein
h3: Major capsid protein
j1: Major capsid protein
j2: Major capsid protein
j3: Major capsid protein
k1: Major capsid protein
k2: Major capsid protein
k3: Major capsid protein
m1: Major capsid protein
m2: Major capsid protein
m3: Major capsid protein
n1: Major capsid protein
n2: Major capsid protein
n3: Major capsid protein
p1: Major capsid protein
p2: Major capsid protein
p3: Major capsid protein
r1: Major capsid protein
r2: Major capsid protein
r3: Major capsid protein
s1: VP38
s2: VP38
s3: VP38
s4: VP38
s5: VP38
s6: VP38
t1: VP38
t2: VP38
t3: VP38
t4: VP38
t5: VP38
t6: VP38
t7: VP38
y2: VP137
y4: VP88
y5: VP59
y6: VP139
y7: VP38
y8: VP38
J2: Major capsid protein
y1: VP137
y3: Penton protein (VP14)
c1: Major capsid protein
c2: Major capsid protein
c3: Major capsid protein
q1: Major capsid protein
q2: Major capsid protein
q3: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)6,703,736144
Polymers6,703,736144
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 7 types, 144 molecules A1A2A3B1B2B3C1C2C3D1D2D3E1E2E3F1F2F3G1G2G3H1H2H3I1I2I3J1J3K1...

#1: Protein ...
Major capsid protein / VP72


Mass: 50573.141 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Source: (natural) Singapore grouper iridovirus / References: UniProt: Q5YFJ3
#2: Protein
VP38


Mass: 19070.715 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Singapore grouper iridovirus / References: UniProt: Q5YFM7
#3: Protein VP137


Mass: 49777.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Singapore grouper iridovirus / References: UniProt: Q5YFC8
#4: Protein VP88


Mass: 54052.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Singapore grouper iridovirus / References: UniProt: Q5YFH7
#5: Protein VP59


Mass: 16343.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Singapore grouper iridovirus / References: UniProt: Q5YFK6
#6: Protein VP139


Mass: 11354.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Singapore grouper iridovirus / References: UniProt: Q5YFC6
#7: Protein Penton protein (VP14)


Mass: 15872.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Singapore grouper iridovirus / References: UniProt: Q5YFQ1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Singapore grouper iridovirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Singapore grouper iridovirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37161 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 82.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022461453
ELECTRON MICROSCOPYf_angle_d0.5082630210
ELECTRON MICROSCOPYf_chiral_restr0.04271938
ELECTRON MICROSCOPYf_plane_restr0.003282093
ELECTRON MICROSCOPYf_dihedral_angle_d13.8189163367

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