SMTL ID : 6ab6.2 (3 other biounits)

Cryo-EM structure of T=3 Penaeus vannamei nodavirus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-15-mer

Ligands

30 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: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:E.118, B:D.146, B:D.151 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 CA.7: 4 residues within 4Å: Chain D: D.148, D.151 Chain E: E.118, N.250 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Metal complexes: D:D.148, D:D.151, D:D.151, E:E.118 CA.8: 4 residues within 4Å: Chain D: D.146, D.151 Chain E: E.118, Q.248 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Metal complexes: D:D.146, D:D.151, E:E.118 CA.9: 6 residues within 4Å: Chain D: E.118, Q.248 Chain F: D.146, D.148, D.151 Ligands: CA.12 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain F Metal complexes: D:E.118, F:D.146, F:D.146, F:D.151 CA.10: 5 residues within 4Å: Chain E: D.146, D.148, D.151 Chain F: E.118, Q.248 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Metal complexes: E:D.146, E:D.151, F:E.118 CA.11: 4 residues within 4Å: Chain E: D.148, D.151 Chain F: E.118, N.250 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.148, E:D.151, E:D.151 CA.12: 7 residues within 4Å: Chain D: E.118, T.196, Q.248, N.250 Chain F: D.148, D.151 Ligands: CA.9 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.148, F:D.151, F:D.151 CA.13: 4 residues within 4Å: Chain G: D.148, D.151 Chain H: E.118, N.250 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G Metal complexes: H:E.118, G:D.148, G:D.151, G:D.151 CA.14: 4 residues within 4Å: Chain G: D.146, D.151 Chain H: E.118, Q.248 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G Metal complexes: H:E.118, G:D.146, G:D.151 CA.15: 6 residues within 4Å: Chain G: E.118, Q.248 Chain I: D.146, D.148, D.151 Ligands: CA.18 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain G Metal complexes: I:D.146, I:D.146, I:D.151, G:E.118 CA.16: 5 residues within 4Å: Chain H: D.146, D.148, D.151 Chain I: E.118, Q.248 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain I Metal complexes: H:D.146, H:D.151, I:E.118 CA.17: 4 residues within 4Å: Chain H: D.148, D.151 Chain I: E.118, N.250 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.148, H:D.151, H:D.151 CA.18: 7 residues within 4Å: Chain G: E.118, T.196, Q.248, N.250 Chain I: D.148, D.151 Ligands: CA.15 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.148, I:D.151, I:D.151 CA.19: 4 residues within 4Å: Chain J: D.148, D.151 Chain K: E.118, N.250 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Metal complexes: J:D.148, J:D.151, J:D.151, K:E.118 CA.20: 4 residues within 4Å: Chain J: D.146, D.151 Chain K: E.118, Q.248 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain K Metal complexes: J:D.146, J:D.151, K:E.118 CA.21: 6 residues within 4Å: Chain J: E.118, Q.248 Chain L: D.146, D.148, D.151 Ligands: CA.24 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain J Metal complexes: L:D.146, L:D.146, L:D.151, J:E.118 CA.22: 5 residues within 4Å: Chain K: D.146, D.148, D.151 Chain L: E.118, Q.248 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K Metal complexes: L:E.118, K:D.146, K:D.151 CA.23: 4 residues within 4Å: Chain K: D.148, D.151 Chain L: E.118, N.250 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.148, K:D.151, K:D.151 CA.24: 7 residues within 4Å: Chain J: E.118, T.196, Q.248, N.250 Chain L: D.148, D.151 Ligands: CA.21 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:D.148, L:D.151, L:D.151 CA.25: 4 residues within 4Å: Chain M: D.148, D.151 Chain N: E.118, N.250 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Metal complexes: M:D.148, M:D.151, M:D.151, N:E.118 CA.26: 4 residues within 4Å: Chain M: D.146, D.151 Chain N: E.118, Q.248 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain N Metal complexes: M:D.146, M:D.151, N:E.118 CA.27: 6 residues within 4Å: Chain M: E.118, Q.248 Chain O: D.146, D.148, D.151 Ligands: CA.30 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain O Metal complexes: M:E.118, O:D.146, O:D.146, O:D.151 CA.28: 5 residues within 4Å: Chain N: D.146, D.148, D.151 Chain O: E.118, Q.248 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O Metal complexes: N:D.146, N:D.151, O:E.118 CA.29: 4 residues within 4Å: Chain N: D.148, D.151 Chain O: E.118, N.250 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:D.148, N:D.151, N:D.151 CA.30: 7 residues within 4Å: Chain M: E.118, T.196, Q.248, N.250 Chain O: D.148, D.151 Ligands: CA.27 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:D.148, O:D.151, O: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: ABCDEFGHIJKLMNO

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

Capsid protein

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