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

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

7 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.114, Q.244, N.246 Chain C: D.144, D.147 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:D.144, C:D.147, C:D.147, A:E.114, A:E.114 CA.2: 5 residues within 4Å: Chain A: D.142, D.144, D.147 Chain B: E.114, Q.244 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.142, A:D.142, A:D.147, B:E.114 CA.3: 7 residues within 4Å: Chain A: D.144, D.147 Chain B: E.114, 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: 7 residues within 4Å: Chain A: E.114, Q.244, N.246 Chain C: D.142, D.144, D.147, Q.165 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.142, C:D.142, C:D.147 CA.5: 8 residues within 4Å: Chain A: D.186, D.187 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.6: 6 residues within 4Å: Chain B: D.142, D.144, D.147, Q.165 Chain C: E.114, Q.244 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.142, B:D.142, B:D.147 CA.7: 6 residues within 4Å: Chain B: D.144, D.147, R.200 Chain C: E.114, Q.244, N.246 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:D.144, B:D.147, B:D.147, C:E.114, C: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) full VLP. To Be Published

Release Date

2019-05-01

Peptides

Capsid protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Capsid protein

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