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

Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-15-mer

Ligands

35 x CA: CALCIUM ION(Non-covalent)

CA.1: 8 residues within 4Å: Chain A: E.114, Y.191, G.193, K.196, Q.244, N.246 Chain C: D.144, D.147 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.144, C:D.147, A:E.114 CA.2: 6 residues within 4Å: Chain A: D.142, D.144, D.147, Q.165 Chain B: E.114, Q.244 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:E.114, A:D.142, A:D.142, A:D.147 CA.3: 8 residues within 4Å: Chain A: D.144, D.147 Chain B: E.114, Y.191, G.193, K.196, Q.244, N.246 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.144, A:D.147, A:D.147, B:E.114 CA.4: 9 residues within 4Å: Chain A: D.186, D.187, Q.188 Chain B: D.186, D.187, Q.188 Chain C: D.186, D.187, Q.188 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.187 CA.5: 6 residues within 4Å: Chain A: E.114, Q.244 Chain C: D.142, D.144, D.147, Q.161 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.142, C:D.142, C:D.147, A:E.114 CA.6: 5 residues within 4Å: Chain B: D.142, D.144, D.147, Q.165 Chain C: Q.244 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.142, B:D.142, B:D.147 CA.7: 8 residues within 4Å: Chain B: D.144, D.147, R.200 Chain C: E.114, T.192, G.193, Q.244, N.246 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Metal complexes: C:E.114, C:E.114, B:D.144, B:D.147, B:D.147 CA.8: 8 residues within 4Å: Chain D: E.114, Y.191, G.193, K.196, Q.244, N.246 Chain F: D.144, D.147 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Metal complexes: F:D.144, F:D.147, D:E.114 CA.9: 6 residues within 4Å: Chain D: D.142, D.144, D.147, Q.165 Chain E: E.114, Q.244 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Metal complexes: D:D.142, D:D.142, D:D.147, E:E.114 CA.10: 8 residues within 4Å: Chain D: D.144, D.147 Chain E: E.114, Y.191, G.193, K.196, Q.244, N.246 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Metal complexes: D:D.144, D:D.147, D:D.147, E:E.114 CA.11: 9 residues within 4Å: Chain D: D.186, D.187, Q.188 Chain E: D.186, D.187, Q.188 Chain F: D.186, D.187, Q.188 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.187 CA.12: 6 residues within 4Å: Chain D: E.114, Q.244 Chain F: D.142, D.144, D.147, Q.161 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain F Metal complexes: D:E.114, F:D.142, F:D.142, F:D.147 CA.13: 5 residues within 4Å: Chain E: D.142, D.144, D.147, Q.165 Chain F: Q.244 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.142, E:D.142, E:D.147 CA.14: 8 residues within 4Å: Chain E: D.144, D.147, R.200 Chain F: E.114, T.192, G.193, Q.244, N.246 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Metal complexes: E:D.144, E:D.147, E:D.147, F:E.114, F:E.114 CA.15: 8 residues within 4Å: Chain G: E.114, Y.191, G.193, K.196, Q.244, N.246 Chain I: D.144, D.147 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G Metal complexes: I:D.144, I:D.147, G:E.114 CA.16: 6 residues within 4Å: Chain G: D.142, D.144, D.147, Q.165 Chain H: E.114, Q.244 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G Metal complexes: H:E.114, G:D.142, G:D.142, G:D.147 CA.17: 8 residues within 4Å: Chain G: D.144, D.147 Chain H: E.114, Y.191, G.193, K.196, Q.244, N.246 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Metal complexes: G:D.144, G:D.147, G:D.147, H:E.114 CA.18: 9 residues within 4Å: Chain G: D.186, D.187, Q.188 Chain H: D.186, D.187, Q.188 Chain I: D.186, D.187, Q.188 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.187 CA.19: 6 residues within 4Å: Chain G: E.114, Q.244 Chain I: D.142, D.144, D.147, Q.161 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain I Metal complexes: G:E.114, I:D.142, I:D.142, I:D.147 CA.20: 5 residues within 4Å: Chain H: D.142, D.144, D.147, Q.165 Chain I: Q.244 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.142, H:D.142, H:D.147 CA.21: 8 residues within 4Å: Chain H: D.144, D.147, R.200 Chain I: E.114, T.192, G.193, Q.244, N.246 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain I Metal complexes: H:D.144, H:D.147, H:D.147, I:E.114, I:E.114 CA.22: 8 residues within 4Å: Chain J: E.114, Y.191, G.193, K.196, Q.244, N.246 Chain L: D.144, D.147 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain L Metal complexes: J:E.114, L:D.144, L:D.147 CA.23: 6 residues within 4Å: Chain J: D.142, D.144, D.147, Q.165 Chain K: E.114, Q.244 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Metal complexes: J:D.142, J:D.142, J:D.147, K:E.114 CA.24: 8 residues within 4Å: Chain J: D.144, D.147 Chain K: E.114, Y.191, G.193, K.196, Q.244, N.246 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Metal complexes: J:D.144, J:D.147, J:D.147, K:E.114 CA.25: 9 residues within 4Å: Chain J: D.186, D.187, Q.188 Chain K: D.186, D.187, Q.188 Chain L: D.186, D.187, Q.188 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.187 CA.26: 6 residues within 4Å: Chain J: E.114, Q.244 Chain L: D.142, D.144, D.147, Q.161 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain L Metal complexes: J:E.114, L:D.142, L:D.142, L:D.147 CA.27: 5 residues within 4Å: Chain K: D.142, D.144, D.147, Q.165 Chain L: Q.244 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.142, K:D.142, K:D.147 CA.28: 8 residues within 4Å: Chain K: D.144, D.147, R.200 Chain L: E.114, T.192, G.193, Q.244, N.246 5 PLIP interactions: 3 interactions with chain K, 2 interactions with chain L Metal complexes: K:D.144, K:D.147, K:D.147, L:E.114, L:E.114 CA.29: 8 residues within 4Å: Chain M: E.114, Y.191, G.193, K.196, Q.244, N.246 Chain O: D.144, D.147 3 PLIP interactions: 2 interactions with chain O, 1 interactions with chain M Metal complexes: O:D.144, O:D.147, M:E.114 CA.30: 6 residues within 4Å: Chain M: D.142, D.144, D.147, Q.165 Chain N: E.114, Q.244 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Metal complexes: M:D.142, M:D.142, M:D.147, N:E.114 CA.31: 8 residues within 4Å: Chain M: D.144, D.147 Chain N: E.114, Y.191, G.193, K.196, Q.244, N.246 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain M Metal complexes: N:E.114, M:D.144, M:D.147, M:D.147 CA.32: 9 residues within 4Å: Chain M: D.186, D.187, Q.188 Chain N: D.186, D.187, Q.188 Chain O: D.186, D.187, Q.188 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.187 CA.33: 6 residues within 4Å: Chain M: E.114, Q.244 Chain O: D.142, D.144, D.147, Q.161 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain O Metal complexes: M:E.114, O:D.142, O:D.142, O:D.147 CA.34: 5 residues within 4Å: Chain N: D.142, D.144, D.147, Q.165 Chain O: Q.244 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:D.142, N:D.142, N:D.147 CA.35: 8 residues within 4Å: Chain N: D.144, D.147, R.200 Chain O: E.114, T.192, G.193, Q.244, N.246 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain O Metal complexes: N:D.144, N:D.147, N:D.147, O:E.114, O:E.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, W.H. et al., Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP. To Be Published

Release Date

2019-05-01

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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