SMTL ID : 8yf6.3 (3 other biounits)

Cryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH8.0 (3.23A)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.130, D.133 Chain B: Q.100, S.170, E.213 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:S.170, B:E.213, A:D.130, A:D.133 CA.2: 5 residues within 4Å: Chain A: Q.100, S.170, E.213 Chain C: D.130, D.133 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Metal complexes: A:S.170, A:E.213, C:D.130, C:D.133, C:D.133 CA.3: 5 residues within 4Å: Chain B: D.130, D.133 Chain C: Q.100, S.170, E.213 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:D.130, B:D.133, C:S.170, C:E.213, C:E.213 CA.4: 5 residues within 4Å: Chain D: D.130, D.133 Chain E: Q.100, S.170, E.213 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Metal complexes: E:S.170, E:E.213, D:D.130, D:D.133 CA.5: 5 residues within 4Å: Chain D: Q.100, S.170, E.213 Chain F: D.130, D.133 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Metal complexes: D:S.170, D:E.213, F:D.130, F:D.133, F:D.133 CA.6: 5 residues within 4Å: Chain E: D.130, D.133 Chain F: Q.100, S.170, E.213 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Metal complexes: F:S.170, F:E.213, F:E.213, E:D.130, E:D.133 CA.7: 5 residues within 4Å: Chain G: D.130, D.133 Chain H: Q.100, S.170, E.213 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H Metal complexes: G:D.130, G:D.133, H:S.170, H:E.213 CA.8: 5 residues within 4Å: Chain G: Q.100, S.170, E.213 Chain I: D.130, D.133 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain G Metal complexes: I:D.130, I:D.133, I:D.133, G:S.170, G:E.213 CA.9: 5 residues within 4Å: Chain H: D.130, D.133 Chain I: Q.100, S.170, E.213 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain I Metal complexes: H:D.130, H:D.133, I:S.170, I:E.213, I:E.213 CA.10: 5 residues within 4Å: Chain J: D.130, D.133 Chain K: Q.100, S.170, E.213 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain J Metal complexes: K:S.170, K:E.213, J:D.130, J:D.133 CA.11: 5 residues within 4Å: Chain J: Q.100, S.170, E.213 Chain L: D.130, D.133 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain J Metal complexes: L:D.130, L:D.133, L:D.133, J:S.170, J:E.213 CA.12: 5 residues within 4Å: Chain K: D.130, D.133 Chain L: Q.100, S.170, E.213 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain L Metal complexes: K:D.130, K:D.133, L:S.170, L:E.213, L:E.213 CA.13: 5 residues within 4Å: Chain M: D.130, D.133 Chain N: Q.100, S.170, E.213 4 PLIP interactions: 2 interactions with chain N, 2 interactions with chain M Metal complexes: N:S.170, N:E.213, M:D.130, M:D.133 CA.14: 5 residues within 4Å: Chain M: Q.100, S.170, E.213 Chain O: D.130, D.133 5 PLIP interactions: 2 interactions with chain M, 3 interactions with chain O Metal complexes: M:S.170, M:E.213, O:D.130, O:D.133, O:D.133 CA.15: 5 residues within 4Å: Chain N: D.130, D.133 Chain O: Q.100, S.170, E.213 5 PLIP interactions: 3 interactions with chain O, 2 interactions with chain N Metal complexes: O:S.170, O:E.213, O:E.213, N:D.130, N:D.133 CA.16: 5 residues within 4Å: Chain P: D.130, D.133 Chain Q: Q.100, S.170, E.213 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain Q Metal complexes: P:D.130, P:D.133, Q:S.170, Q:E.213 CA.17: 5 residues within 4Å: Chain P: Q.100, S.170, E.213 Chain R: D.130, D.133 5 PLIP interactions: 3 interactions with chain R, 2 interactions with chain P Metal complexes: R:D.130, R:D.133, R:D.133, P:S.170, P:E.213 CA.18: 5 residues within 4Å: Chain Q: D.130, D.133 Chain R: Q.100, S.170, E.213 5 PLIP interactions: 3 interactions with chain R, 2 interactions with chain Q Metal complexes: R:S.170, R:E.213, R:E.213, Q:D.130, Q:D.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sterbova, P. et al., Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy. Acs Infect Dis. (2024)

Release Date

2024-08-14

Peptides

Capsid protein alpha: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

P
A

Q
B

R
C

Capsid protein alpha

Related Entries With Identical Sequence