SMTL ID : 6ab6.1 (3 other biounits)

Cryo-EM structure of T=3 Penaeus vannamei nodavirus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.148, D.151 Chain B: E.118, N.250 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.148, A:D.151, A:D.151, B:E.118 CA.2: 4 residues within 4Å: Chain A: D.146, D.151 Chain B: E.118, Q.248 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.146, A:D.151, B:E.118 CA.3: 6 residues within 4Å: Chain A: E.118, Q.248 Chain C: D.146, D.148, D.151 Ligands: CA.6 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.146, C:D.146, C:D.151, A:E.118 CA.4: 5 residues within 4Å: Chain B: D.146, D.148, D.151 Chain C: E.118, Q.248 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Metal complexes: B:D.146, B:D.151, C:E.118 CA.5: 4 residues within 4Å: Chain B: D.148, D.151 Chain C: E.118, N.250 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.148, B:D.151, B:D.151 CA.6: 7 residues within 4Å: Chain A: E.118, T.196, Q.248, N.250 Chain C: D.148, D.151 Ligands: CA.3 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.148, C:D.151, C:D.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, N.C. et al., The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol (2019)

Release Date

2019-03-20

Peptides

Capsid protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Capsid protein

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