8HIF

One asymmetric unit of Singapore grouper iridovirus capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly.

Zhao, Z.Huang, Y.Liu, C.Zhu, D.Gao, S.Liu, S.Peng, R.Zhang, Y.Huang, X.Qi, J.Wong, C.C.L.Zhang, X.Wang, P.Qin, Q.Gao, G.F.

(2023) Nat Commun 14: 2050-2050

  • DOI: https://doi.org/10.1038/s41467-023-37681-9
  • Primary Citation of Related Structures:  
    8HIF

  • PubMed 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 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.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein
A [auth A1],
AA [auth I3],
AB [auth R3],
AC [auth a2],
AD [auth m1],
B [auth A2],
BA [auth J1],
BB [auth S1],
BC [auth a3],
BD [auth m2],
C [auth A3],
CA [auth J3],
CB [auth S2],
CC [auth b1],
CD [auth m3],
D [auth B1],
DA [auth K1],
DB [auth S3],
DC [auth b2],
DD [auth n1],
E [auth B2],
EA [auth K2],
EB [auth T1],
EC [auth b3],
ED [auth n2],
F [auth B3],
FA [auth K3],
FB [auth T2],
FC [auth d1],
FD [auth n3],
FE [auth J2],
G [auth C1],
GA [auth L1],
GB [auth T3],
GC [auth d2],
GD [auth p1],
H [auth C2],
HA [auth L2],
HB [auth U1],
HC [auth d3],
HD [auth p2],
I [auth C3],
IA [auth L3],
IB [auth U2],
IC [auth e1],
ID [auth p3],
IE [auth c1],
J [auth D1],
JA [auth M1],
JB [auth U3],
JC [auth e2],
JD [auth r1],
JE [auth c2],
K [auth D2],
KA [auth M2],
KB [auth V1],
KC [auth e3],
KD [auth r2],
KE [auth c3],
L [auth D3],
LA [auth M3],
LB [auth V2],
LC [auth f1],
LD [auth r3],
LE [auth q1],
M [auth E1],
MA [auth N1],
MB [auth V3],
MC [auth f2],
ME [auth q2],
N [auth E2],
NA [auth N2],
NB [auth W1],
NC [auth f3],
NE [auth q3],
O [auth E3],
OA [auth N3],
OB [auth W2],
OC [auth g1],
P [auth F1],
PA [auth O1],
PB [auth W3],
PC [auth g2],
Q [auth F2],
QA [auth O2],
QB [auth X1],
QC [auth g3],
R [auth F3],
RA [auth O3],
RB [auth X2],
RC [auth h1],
S [auth G1],
SA [auth P1],
SB [auth X3],
SC [auth h2],
T [auth G2],
TA [auth P2],
TB [auth Y1],
TC [auth h3],
U [auth G3],
UA [auth P3],
UB [auth Y2],
UC [auth j1],
V [auth H1],
VA [auth Q1],
VB [auth Y3],
VC [auth j2],
W [auth H2],
WA [auth Q2],
WB [auth Z1],
WC [auth j3],
X [auth H3],
XA [auth Q3],
XB [auth Z2],
XC [auth k1],
Y [auth I1],
YA [auth R1],
YB [auth Z3],
YC [auth k2],
Z [auth I2],
ZA [auth R2],
ZB [auth a1],
ZC [auth k3]
463Singapore grouper iridovirusMutation(s): 0 
UniProt
Find proteins for Q5YFJ3 (Singapore grouper iridovirus)
Explore Q5YFJ3 
Go to UniProtKB:  Q5YFJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YFJ3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP38170Singapore grouper iridovirusMutation(s): 0 
UniProt
Find proteins for Q5YFM7 (Singapore grouper iridovirus)
Explore Q5YFM7 
Go to UniProtKB:  Q5YFM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YFM7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP137GE [auth y1],
ZD [auth y2]
461Singapore grouper iridovirusMutation(s): 0 
UniProt
Find proteins for Q5YFC8 (Singapore grouper iridovirus)
Explore Q5YFC8 
Go to UniProtKB:  Q5YFC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YFC8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VP88AE [auth y4]506Singapore grouper iridovirusMutation(s): 0 
UniProt
Find proteins for Q5YFH7 (Singapore grouper iridovirus)
Explore Q5YFH7 
Go to UniProtKB:  Q5YFH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YFH7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
VP59BE [auth y5]146Singapore grouper iridovirusMutation(s): 0 
UniProt
Find proteins for Q5YFK6 (Singapore grouper iridovirus)
Explore Q5YFK6 
Go to UniProtKB:  Q5YFK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YFK6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
VP139CE [auth y6]103Singapore grouper iridovirusMutation(s): 0 
UniProt
Find proteins for Q5YFC6 (Singapore grouper iridovirus)
Explore Q5YFC6 
Go to UniProtKB:  Q5YFC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YFC6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Penton protein (VP14)HE [auth y3]141Singapore grouper iridovirusMutation(s): 0 
UniProt
Find proteins for Q5YFQ1 (Singapore grouper iridovirus)
Explore Q5YFQ1 
Go to UniProtKB:  Q5YFQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YFQ1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release