SMTL ID : 9mxc.1 (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-1-1-1-1-mer

Ligands

1 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: 24 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 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2 17 PLIP interactions: 16 interactions with chain A, 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, C:Q.247 Salt bridges: A:K.92

1 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

3 x NA: SODIUM ION

NA.3: 5 residues within 4Å: Chain A: T.7, A.8, T.9, D.10, N.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.7, A:T.7 NA.4: 7 residues within 4Å: Chain A: R.252, P.253 Chain B: H.119, L.150, D.152, T.154, F.162 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.152 Water bridges: A:R.252 NA.5: 7 residues within 4Å: Chain C: Q.89, M.177, F.178, N.179, N.180, D.181, A.187 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.179, C:N.179, C:D.181

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: A
viral protein 2: B
viral protein 3: C
viral protein 4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

viral protein 1

viral protein 2

viral protein 3

viral protein 4

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