SMTL ID : 6thd.3 (3 other biounits)

Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-mer

Ligands

12 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: 6 residues within 4Å: Chain D: G.1, N.9, Y.10, N.11, I.13, Y.15 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.10, D:N.11, D:I.13 Hydrogen bonds: D:G.1 MYR.5: 12 residues within 4Å: Chain E: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain G: I.24 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:F.121, E:Y.145, E:Y.145, E:Y.145, E:V.182, E:Y.191, G:I.24 Hydrogen bonds: E:F.99 Salt bridges: E:R.100 MYR.8: 13 residues within 4Å: Chain A: L.7, D.9, A.10 Chain D: N.14, Y.15, Y.16, S.17 Chain H: G.1, N.9, Y.10, N.11, I.13, Y.15 9 PLIP interactions: 2 interactions with chain A, 4 interactions with chain H, 3 interactions with chain D Hydrophobic interactions: A:L.7, A:A.10, H:Y.10, H:N.11, H:I.13, D:Y.15 Hydrogen bonds: H:G.1, D:N.14, D:Y.16 MYR.9: 12 residues within 4Å: Chain I: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain K: I.24 9 PLIP interactions: 1 interactions with chain K, 8 interactions with chain I Hydrophobic interactions: K:I.24, I:F.121, I:Y.145, I:Y.145, I:Y.145, I:V.182, I:Y.191 Hydrogen bonds: I:F.99 Salt bridges: I:R.100 MYR.12: 13 residues within 4Å: Chain L: G.1, N.9, Y.10, N.11, I.13, Y.15 Chain M: L.7, D.9, A.10 Chain P: N.14, Y.15, Y.16, S.17 9 PLIP interactions: 4 interactions with chain L, 2 interactions with chain M, 3 interactions with chain P Hydrophobic interactions: L:Y.10, L:N.11, L:I.13, M:L.7, M:A.10, P:Y.15 Hydrogen bonds: L:G.1, P:N.14, P:Y.16 MYR.13: 12 residues within 4Å: Chain M: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain O: I.24 9 PLIP interactions: 8 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: M:F.121, M:Y.145, M:Y.145, M:Y.145, M:V.182, M:Y.191, O:I.24 Hydrogen bonds: M:F.99 Salt bridges: M:R.100 MYR.16: 6 residues within 4Å: Chain P: G.1, N.9, Y.10, N.11, I.13, Y.15 4 PLIP interactions: 4 interactions with chain P Hydrophobic interactions: P:Y.10, P:N.11, P:I.13 Hydrogen bonds: P:G.1 MYR.17: 12 residues within 4Å: Chain Q: I.97, D.98, F.99, R.100, F.121, Y.145, V.182, M.185, Y.191, N.215, M.220 Chain S: I.24 9 PLIP interactions: 8 interactions with chain Q, 1 interactions with chain S Hydrophobic interactions: Q:F.121, Q:Y.145, Q:Y.145, Q:Y.145, Q:V.182, Q:Y.191, S:I.24 Hydrogen bonds: Q:F.99 Salt bridges: Q:R.100 MYR.20: 6 residues within 4Å: Chain T: G.1, N.9, Y.10, N.11, I.13, Y.15 4 PLIP interactions: 4 interactions with chain T Hydrophobic interactions: T:Y.10, T:N.11, T:I.13 Hydrogen bonds: T:G.1 MYR.21: 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.24: 13 residues within 4Å: Chain Q: L.7, D.9, A.10 Chain T: N.14, Y.15, Y.16, S.17 Chain X: G.1, N.9, Y.10, N.11, I.13, Y.15 9 PLIP interactions: 4 interactions with chain X, 3 interactions with chain T, 2 interactions with chain Q Hydrophobic interactions: X:Y.10, X:N.11, X:I.13, T:Y.15, Q:L.7, Q:A.10 Hydrogen bonds: X:G.1, T:N.14, T:Y.16

12 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.130, A:A.229, 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, B:S.147 Water bridges: B:N.87 SO4.6: 6 residues within 4Å: Chain E: S.128, T.129, G.130, A.229, H.230, Q.231 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.130, E:A.229, E:Q.231 Salt bridges: E:H.230 SO4.7: 4 residues within 4Å: Chain F: A.85, N.88, G.146, S.147 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.88, F:N.88, F:S.147, F:S.147 Water bridges: F:N.87, F:T.89 SO4.10: 6 residues within 4Å: Chain I: S.128, T.129, G.130, A.229, H.230, Q.231 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:G.130, I:A.229, I:Q.231 Salt bridges: I:H.230 SO4.11: 4 residues within 4Å: Chain J: A.85, N.88, G.146, S.147 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:N.88, J:N.88, J:S.147, J:S.147 Water bridges: J:N.87, J:T.89 SO4.14: 6 residues within 4Å: Chain M: S.128, T.129, G.130, A.229, H.230, Q.231 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:G.130, M:A.229, M:Q.231 Salt bridges: M:H.230 SO4.15: 4 residues within 4Å: Chain N: A.85, N.88, G.146, S.147 6 PLIP interactions: 6 interactions with chain N Hydrogen bonds: N:N.88, N:N.88, N:S.147, N:S.147 Water bridges: N:N.87, N:T.89 SO4.18: 6 residues within 4Å: Chain Q: S.128, T.129, G.130, A.229, H.230, Q.231 4 PLIP interactions: 4 interactions with chain Q Hydrogen bonds: Q:G.130, Q:A.229, Q:Q.231 Salt bridges: Q:H.230 SO4.19: 4 residues within 4Å: Chain R: A.85, N.88, G.146, S.147 6 PLIP interactions: 6 interactions with chain R Hydrogen bonds: R:N.88, R:N.88, R:S.147, R:S.147 Water bridges: R:N.87, R:T.89 SO4.22: 6 residues within 4Å: Chain U: S.128, T.129, G.130, A.229, H.230, Q.231 4 PLIP interactions: 4 interactions with chain U Hydrogen bonds: U:G.130, U:A.229, U:Q.231 Salt bridges: U:H.230 SO4.23: 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, V:S.147 Water bridges: V:N.87

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: AEIMQU
Genome polyprotein: BFJNRV
Genome polyprotein: CGKOSW
Genome polyprotein: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

E
1

I
1

M
1

Q
1

U
1

B
2

F
2

J
2

N
2

R
2

V
2

C
3

G
3

K
3

O
3

S
3

W
3

D
4

H
4

L
4

P
4

T
4

X
4

Genome polyprotein

Genome polyprotein

Genome polyprotein

Genome polyprotein

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