8HIF image
Entry Detail
PDB ID:
8HIF
EMDB ID:
Keywords:
Title:
One asymmetric unit of Singapore grouper iridovirus capsid
Biological Source:
PDB Version:
Deposition Date:
2022-11-20
Release Date:
2023-04-19
Method Details:
Experimental Method:
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Major capsid protein
Chain IDs:A (auth: A1), B (auth: A2), C (auth: A3), D (auth: B1), E (auth: B2), F (auth: B3), G (auth: C1), H (auth: C2), I (auth: C3), J (auth: D1), K (auth: D2), L (auth: D3), M (auth: E1), N (auth: E2), O (auth: E3), P (auth: F1), Q (auth: F2), R (auth: F3), S (auth: G1), T (auth: G2), U (auth: G3), V (auth: H1), W (auth: H2), X (auth: H3), Y (auth: I1), Z (auth: I2), AA (auth: I3), BA (auth: J1), CA (auth: J3), DA (auth: K1), EA (auth: K2), FA (auth: K3), GA (auth: L1), HA (auth: L2), IA (auth: L3), JA (auth: M1), KA (auth: M2), LA (auth: M3), MA (auth: N1), NA (auth: N2), OA (auth: N3), PA (auth: O1), QA (auth: O2), RA (auth: O3), SA (auth: P1), TA (auth: P2), UA (auth: P3), VA (auth: Q1), WA (auth: Q2), XA (auth: Q3), YA (auth: R1), ZA (auth: R2), AB (auth: R3), BB (auth: S1), CB (auth: S2), DB (auth: S3), EB (auth: T1), FB (auth: T2), GB (auth: T3), HB (auth: U1), IB (auth: U2), JB (auth: U3), KB (auth: V1), LB (auth: V2), MB (auth: V3), NB (auth: W1), OB (auth: W2), PB (auth: W3), QB (auth: X1), RB (auth: X2), SB (auth: X3), TB (auth: Y1), UB (auth: Y2), VB (auth: Y3), WB (auth: Z1), XB (auth: Z2), YB (auth: Z3), ZB (auth: a1), AC (auth: a2), BC (auth: a3), CC (auth: b1), DC (auth: b2), EC (auth: b3), FC (auth: d1), GC (auth: d2), HC (auth: d3), IC (auth: e1), JC (auth: e2), KC (auth: e3), LC (auth: f1), MC (auth: f2), NC (auth: f3), OC (auth: g1), PC (auth: g2), QC (auth: g3), RC (auth: h1), SC (auth: h2), TC (auth: h3), UC (auth: j1), VC (auth: j2), WC (auth: j3), XC (auth: k1), YC (auth: k2), ZC (auth: k3), AD (auth: m1), BD (auth: m2), CD (auth: m3), DD (auth: n1), ED (auth: n2), FD (auth: n3), GD (auth: p1), HD (auth: p2), ID (auth: p3), JD (auth: r1), KD (auth: r2), LD (auth: r3), FE (auth: J2), IE (auth: c1), JE (auth: c2), KE (auth: c3), LE (auth: q1), ME (auth: q2), NE (auth: q3)
Chain Length:463
Number of Molecules:123
Biological Source:Singapore grouper iridovirus
Polymer Type:polypeptide(L)
Description:VP38
Chain IDs:MD (auth: s1), ND (auth: s2), OD (auth: s3), PD (auth: s4), QD (auth: s5), RD (auth: s6), SD (auth: t1), TD (auth: t2), UD (auth: t3), VD (auth: t4), WD (auth: t5), XD (auth: t6), YD (auth: t7), DE (auth: y7), EE (auth: y8)
Chain Length:463
Number of Molecules:15
Biological Source:Singapore grouper iridovirus
Polymer Type:polypeptide(L)
Description:VP137
Chain IDs:ZD (auth: y2), GE (auth: y1)
Chain Length:463
Number of Molecules:2
Biological Source:Singapore grouper iridovirus
Polymer Type:polypeptide(L)
Description:Penton protein (VP14)
Chain IDs:HE (auth: y3)
Chain Length:141
Number of Molecules:1
Biological Source:Singapore grouper iridovirus
Polymer Type:polypeptide(L)
Description:VP88
Chain IDs:AE (auth: y4)
Chain Length:506
Number of Molecules:1
Biological Source:Singapore grouper iridovirus
Polymer Type:polypeptide(L)
Description:VP59
Chain IDs:BE (auth: y5)
Chain Length:146
Number of Molecules:1
Biological Source:Singapore grouper iridovirus
Polymer Type:polypeptide(L)
Description:VP139
Chain IDs:CE (auth: y6)
Chain Length:103
Number of Molecules:1
Biological Source:Singapore grouper iridovirus
Ligand Molecules
Primary Citation
Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly.
Nat Commun 14 2050 2050 (2023)
PMID: 37041173 DOI: 10.1038/s41467-023-37681-9

Abstact

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.

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Disease

Primary Citation of related structures