SMTL ID : 9mxc.2 (3 other biounits)

Cryo-EM Structure of Human Enterovirus D68 USA/IL/14-18952 in Complex with Fc-MFSD6(L3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-mer

Ligands

5 x ASN- LEU- LEU- GLU- THR- ARG- LEU- ASN- VAL: Major facilitator superfamily domain-containing protein 6

ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.1: 26 residues within 4Å: Chain A: K.92, T.94, N.96, R.98, T.150, G.151, F.200, A.201, G.202, G.207, L.208, Y.209, I.211, N.212, P.213, T.216, N.219, I.262, A.263 Chain C: A.241, A.244, A.245, Q.247 Chain G: N.179, D.181 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2 19 PLIP interactions: 16 interactions with chain A, 2 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: A:L.208, A:I.211, A:I.211, A:P.213, A:A.263 Hydrogen bonds: A:K.92, A:T.94, A:G.151, A:A.201, A:A.201, A:L.208, A:L.208, A:L.208, A:T.216, A:N.219, G:N.179, G:D.181, C:Q.247 Salt bridges: A:K.92 ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.6: 26 residues within 4Å: Chain E: K.92, T.94, N.96, R.98, T.150, G.151, F.200, A.201, G.202, G.207, L.208, Y.209, I.211, N.212, P.213, T.216, N.219, I.262, A.263 Chain G: A.241, A.244, A.245, Q.247 Chain K: N.179, D.181 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.7 18 PLIP interactions: 2 interactions with chain K, 16 interactions with chain E Hydrogen bonds: K:N.179, K:D.181, E:K.92, E:T.94, E:G.151, E:A.201, E:A.201, E:L.208, E:L.208, E:L.208, E:T.216, E:N.219 Hydrophobic interactions: E:L.208, E:I.211, E:I.211, E:P.213, E:A.263 Salt bridges: E:K.92 ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.11: 26 residues within 4Å: Chain I: K.92, T.94, N.96, R.98, T.150, G.151, F.200, A.201, G.202, G.207, L.208, Y.209, I.211, N.212, P.213, T.216, N.219, I.262, A.263 Chain K: A.241, A.244, A.245, Q.247 Chain O: N.179, D.181 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.12 17 PLIP interactions: 16 interactions with chain I, 1 interactions with chain O Hydrophobic interactions: I:L.208, I:I.211, I:I.211, I:P.213, I:A.263 Hydrogen bonds: I:K.92, I:T.94, I:G.151, I:A.201, I:A.201, I:L.208, I:L.208, I:L.208, I:T.216, I:N.219, O:N.179 Salt bridges: I:K.92 ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.16: 26 residues within 4Å: Chain M: K.92, T.94, N.96, R.98, T.150, G.151, F.200, A.201, G.202, G.207, L.208, Y.209, I.211, N.212, P.213, T.216, N.219, I.262, A.263 Chain O: A.241, A.244, A.245, Q.247 Chain S: N.179, D.181 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.17 17 PLIP interactions: 16 interactions with chain M, 1 interactions with chain S Hydrophobic interactions: M:L.208, M:I.211, M:I.211, M:P.213, M:A.263 Hydrogen bonds: M:K.92, M:T.94, M:G.151, M:A.201, M:A.201, M:L.208, M:L.208, M:L.208, M:T.216, M:N.219, S:N.179 Salt bridges: M:K.92 ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.21: 26 residues within 4Å: Chain C: N.179, D.181 Chain Q: K.92, T.94, N.96, R.98, T.150, G.151, F.200, A.201, G.202, G.207, L.208, Y.209, I.211, N.212, P.213, T.216, N.219, I.262, A.263 Chain S: A.241, A.244, A.245, Q.247 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.22 19 PLIP interactions: 2 interactions with chain C, 16 interactions with chain Q, 1 interactions with chain S Hydrogen bonds: C:N.179, C:D.181, Q:K.92, Q:T.94, Q:G.151, Q:A.201, Q:A.201, Q:L.208, Q:L.208, Q:L.208, Q:T.216, Q:N.219, S:Q.247 Hydrophobic interactions: Q:L.208, Q:I.211, Q:I.211, Q:P.213, Q:A.263 Salt bridges: Q:K.92

5 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.2: 12 residues within 4Å: Chain A: L.208, S.261, A.263, N.264 Chain B: T.126, N.127, T.128, S.129 Chain C: H.240, A.241 Ligands: ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.1, ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.126, B:N.127 NAG-NAG-BMA-MAN-MAN-FUC.7: 12 residues within 4Å: Chain E: L.208, S.261, A.263, N.264 Chain F: T.126, N.127, T.128, S.129 Chain G: H.240, A.241 Ligands: ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.6, ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.6 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.126, F:N.127 NAG-NAG-BMA-MAN-MAN-FUC.12: 12 residues within 4Å: Chain I: L.208, S.261, A.263, N.264 Chain J: T.126, N.127, T.128, S.129 Chain K: H.240, A.241 Ligands: ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.11, ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.11 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:T.126, J:N.127 NAG-NAG-BMA-MAN-MAN-FUC.17: 12 residues within 4Å: Chain M: L.208, S.261, A.263, N.264 Chain N: T.126, N.127, T.128, S.129 Chain O: H.240, A.241 Ligands: ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.16, ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.16 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:T.126, N:N.127 NAG-NAG-BMA-MAN-MAN-FUC.22: 12 residues within 4Å: Chain Q: L.208, S.261, A.263, N.264 Chain R: T.126, N.127, T.128, S.129 Chain S: H.240, A.241 Ligands: ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.21, ASN-LEU-LEU-GLU-THR-ARG-LEU-ASN-VAL.21 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:T.126, R:N.127

15 x NA: SODIUM ION

NA.3: 5 residues within 4Å: Chain A: T.7, A.8, T.9, D.10, N.50 Ligand excluded by PLIP NA.4: 7 residues within 4Å: Chain A: R.252, P.253 Chain B: H.119, L.150, D.152, T.154, F.162 Ligand excluded by PLIP NA.5: 7 residues within 4Å: Chain C: Q.89, M.177, F.178, N.179, N.180, D.181, A.187 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain E: T.7, A.8, T.9, D.10, N.50 Ligand excluded by PLIP NA.9: 7 residues within 4Å: Chain E: R.252, P.253 Chain F: H.119, L.150, D.152, T.154, F.162 Ligand excluded by PLIP NA.10: 7 residues within 4Å: Chain G: Q.89, M.177, F.178, N.179, N.180, D.181, A.187 Ligand excluded by PLIP NA.13: 5 residues within 4Å: Chain I: T.7, A.8, T.9, D.10, N.50 Ligand excluded by PLIP NA.14: 7 residues within 4Å: Chain I: R.252, P.253 Chain J: H.119, L.150, D.152, T.154, F.162 Ligand excluded by PLIP NA.15: 7 residues within 4Å: Chain K: Q.89, M.177, F.178, N.179, N.180, D.181, A.187 Ligand excluded by PLIP NA.18: 5 residues within 4Å: Chain M: T.7, A.8, T.9, D.10, N.50 Ligand excluded by PLIP NA.19: 7 residues within 4Å: Chain M: R.252, P.253 Chain N: H.119, L.150, D.152, T.154, F.162 Ligand excluded by PLIP NA.20: 7 residues within 4Å: Chain O: Q.89, M.177, F.178, N.179, N.180, D.181, A.187 Ligand excluded by PLIP NA.23: 5 residues within 4Å: Chain Q: T.7, A.8, T.9, D.10, N.50 Ligand excluded by PLIP NA.24: 7 residues within 4Å: Chain Q: R.252, P.253 Chain R: H.119, L.150, D.152, T.154, F.162 Ligand excluded by PLIP NA.25: 7 residues within 4Å: Chain S: Q.89, M.177, F.178, N.179, N.180, D.181, A.187 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varanese, L. et al., MFSD6 is an entry receptor for enterovirus D68. Nature (2025)

Release Date

2025-03-26

Peptides

viral protein 1: AEIMQ
viral protein 2: BFJNR
viral protein 3: CGKOS
viral protein 4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

B
B

F
B

J
B

N
B

R
B

C
C

G
C

K
C

O
C

S
C

D
D

H
D

L
D

P
D

T
D

viral protein 1

viral protein 2

viral protein 3

viral protein 4

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