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

Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+2fold focused classification

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-mer

Ligands

10 x MYR: MYRISTIC ACID(Non-covalent)

MYR.1: 12 residues within 4Å: Chain A: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain C: I.24 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.121, A:Y.145, A:Y.145, A:Y.145, A:V.182, A:Y.191, C:I.24 Hydrogen bonds: A:F.99 Salt bridges: A:R.100 MYR.4: 14 residues within 4Å: Chain D: G.1, N.9, Y.10, N.11, I.13, Y.15 Chain M: L.2 Chain U: L.7, D.9, A.10 Chain X: N.14, Y.15, Y.16, S.17 10 PLIP interactions: 4 interactions with chain D, 2 interactions with chain X, 1 interactions with chain M, 3 interactions with chain U Hydrophobic interactions: D:Y.10, D:N.11, D:I.13, X:Y.15, M:L.2, U:L.7, U:A.10 Hydrogen bonds: D:G.1, X:N.14, U:D.9 MYR.5: 12 residues within 4Å: Chain F: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain H: I.24 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: F:F.121, F:Y.145, F:Y.145, F:Y.145, F:V.182, F:Y.191, H:I.24 Hydrogen bonds: F:F.99 Salt bridges: F:R.100 MYR.8: 14 residues within 4Å: Chain A: L.7, D.9, A.10 Chain D: N.14, Y.15, Y.16, S.17 Chain I: G.1, N.9, Y.10, N.11, I.13, Y.15 Chain R: L.2 10 PLIP interactions: 4 interactions with chain I, 1 interactions with chain R, 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: I:Y.10, I:N.11, I:I.13, R:L.2, D:Y.15, A:L.7, A:A.10 Hydrogen bonds: I:G.1, D:N.14, A:D.9 MYR.9: 12 residues within 4Å: Chain K: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain M: I.24 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain M Hydrophobic interactions: K:F.121, K:Y.145, K:Y.145, K:Y.145, K:V.182, K:Y.191, M:I.24 Hydrogen bonds: K:F.99 Salt bridges: K:R.100 MYR.12: 14 residues within 4Å: Chain F: L.7, D.9, A.10 Chain I: N.14, Y.15, Y.16, S.17 Chain N: G.1, N.9, Y.10, N.11, I.13, Y.15 Chain W: L.2 10 PLIP interactions: 4 interactions with chain N, 2 interactions with chain I, 1 interactions with chain W, 3 interactions with chain F Hydrophobic interactions: N:Y.10, N:N.11, N:I.13, I:Y.15, W:L.2, F:L.7, F:A.10 Hydrogen bonds: N:G.1, I:N.14, F:D.9 MYR.13: 12 residues within 4Å: Chain P: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain R: I.24 9 PLIP interactions: 8 interactions with chain P, 1 interactions with chain R Hydrophobic interactions: P:F.121, P:Y.145, P:Y.145, P:Y.145, P:V.182, P:Y.191, R:I.24 Hydrogen bonds: P:F.99 Salt bridges: P:R.100 MYR.16: 14 residues within 4Å: Chain C: L.2 Chain K: L.7, D.9, A.10 Chain N: N.14, Y.15, Y.16, S.17 Chain S: G.1, N.9, Y.10, N.11, I.13, Y.15 10 PLIP interactions: 3 interactions with chain K, 4 interactions with chain S, 1 interactions with chain C, 2 interactions with chain N Hydrophobic interactions: K:L.7, K:A.10, S:Y.10, S:N.11, S:I.13, C:L.2, N:Y.15 Hydrogen bonds: K:D.9, S:G.1, N:N.14 MYR.17: 12 residues within 4Å: Chain U: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain W: I.24 9 PLIP interactions: 8 interactions with chain U, 1 interactions with chain W Hydrophobic interactions: U:F.121, U:Y.145, U:Y.145, U:Y.145, U:V.182, U:Y.191, W:I.24 Hydrogen bonds: U:F.99 Salt bridges: U:R.100 MYR.20: 14 residues within 4Å: Chain H: L.2 Chain P: L.7, D.9, A.10 Chain S: N.14, Y.15, Y.16, S.17 Chain X: G.1, N.9, Y.10, N.11, I.13, Y.15 10 PLIP interactions: 3 interactions with chain P, 4 interactions with chain X, 2 interactions with chain S, 1 interactions with chain H Hydrophobic interactions: P:L.7, P:A.10, X:Y.10, X:N.11, X:I.13, S:Y.15, H:L.2 Hydrogen bonds: P:D.9, X:G.1, S:N.14

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: S.128, T.129, G.130, A.229, H.230, Q.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.130, A:Q.231 Salt bridges: A:H.230 SO4.3: 4 residues within 4Å: Chain B: A.85, N.88, G.146, S.147 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.88, B:N.88, B:S.147 Water bridges: B:N.87, B:T.89 SO4.6: 6 residues within 4Å: Chain F: S.128, T.129, G.130, A.229, H.230, Q.231 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.130, F:Q.231 Salt bridges: F:H.230 SO4.7: 4 residues within 4Å: Chain G: A.85, N.88, G.146, S.147 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:N.88, G:N.88, G:S.147 Water bridges: G:N.87 SO4.10: 6 residues within 4Å: Chain K: S.128, T.129, G.130, A.229, H.230, Q.231 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:G.130, K:Q.231 Salt bridges: K:H.230 SO4.11: 4 residues within 4Å: Chain L: A.85, N.88, G.146, S.147 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:N.88, L:N.88, L:S.147 Water bridges: L:N.87, L:T.89 SO4.14: 6 residues within 4Å: Chain P: S.128, T.129, G.130, A.229, H.230, Q.231 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:G.130, P:Q.231 Salt bridges: P:H.230 SO4.15: 4 residues within 4Å: Chain Q: A.85, N.88, G.146, S.147 5 PLIP interactions: 5 interactions with chain Q Hydrogen bonds: Q:N.88, Q:N.88, Q:S.147 Water bridges: Q:N.87, Q:T.89 SO4.18: 6 residues within 4Å: Chain U: S.128, T.129, G.130, A.229, H.230, Q.231 3 PLIP interactions: 3 interactions with chain U Hydrogen bonds: U:G.130, U:Q.231 Salt bridges: U:H.230 SO4.19: 4 residues within 4Å: Chain V: A.85, N.88, G.146, S.147 5 PLIP interactions: 5 interactions with chain V Hydrogen bonds: V:N.88, V:N.88, V:S.147 Water bridges: V:N.87, V:T.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandler-Bostock, R. et al., Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. Plos Pathog. (2020)

Release Date

2020-12-09

Peptides

Genome polyprotein: AFKPU
Genome polyprotein: BGLQV
Genome polyprotein: CHMRW
Genome polyprotein: DINSX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

F
1

K
1

P
1

U
1

B
2

G
2

L
2

Q
2

V
2

C
3

H
3

M
3

R
3

W
3

D
4

I
4

N
4

S
4

X
4

Genome polyprotein

Genome polyprotein

Genome polyprotein

Genome polyprotein

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