SMTL ID : 8uuq.1

Structure of the Measles virus Fusion protein in the pre-fusion conformation with bound [FIP-HRC]2-PEG11

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

3 x P6S- PHE- PHE- GLY: [FIP-HRC]2-PEG11(Non-covalent)

P6S-PHE-PHE-GLY.1: 17 residues within 4Å: Chain B: W.199, L.258, P.339, I.340, S.341, V.347, N.350, N.353, A.354, K.357 Chain D: P.241, L.242 Chain F: G.348, L.351, G.352, I.355, E.359 19 PLIP interactions: 2 interactions with chain D, 11 interactions with chain B, 6 interactions with chain F Hydrophobic interactions: D:P.241, B:L.258, B:P.339, B:I.340, B:I.340, B:V.347, B:N.350, B:N.353, B:A.354, B:K.357, F:L.351, F:L.351, F:I.355, F:I.355, F:E.359 Hydrogen bonds: D:L.242, B:N.350, F:E.359 pi-Stacking: B:W.199 P6S-PHE-PHE-GLY.2: 18 residues within 4Å: Chain B: G.348, L.351, G.352, I.355, E.359 Chain D: W.199, L.258, P.339, I.340, S.341, V.347, N.350, N.353, A.354, K.357 Chain F: S.240, P.241, L.242 19 PLIP interactions: 5 interactions with chain B, 12 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: B:L.351, B:L.351, B:I.355, B:I.355, B:I.355, D:L.258, D:P.339, D:I.340, D:I.340, D:V.347, D:N.353, D:A.354, D:K.357, F:P.241 Hydrogen bonds: D:P.339, D:N.350, D:N.350, F:L.242 pi-Stacking: D:W.199 P6S-PHE-PHE-GLY.3: 18 residues within 4Å: Chain B: S.240, P.241 Chain D: G.348, L.351, G.352, I.355, E.359 Chain F: W.199, L.258, P.339, I.340, S.341, D.346, V.347, N.350, N.353, A.354, K.357 19 PLIP interactions: 12 interactions with chain F, 1 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: F:L.258, F:P.339, F:I.340, F:I.340, F:V.347, F:N.350, F:N.353, F:A.354, F:K.357, B:P.241, D:L.351, D:L.351, D:I.355, D:I.355, D:I.355, D:E.359 Hydrogen bonds: F:N.350, F:N.350 pi-Stacking: F:W.199

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 8 residues within 4Å: Chain A: H.26, N.29, K.32 Chain B: R.248, G.249, T.251, R.333, D.335 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.335, B:D.335 NAG-NAG-BMA.5: 5 residues within 4Å: Chain A: N.61, T.63 Chain B: E.43, T.44, N.46 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain C: N.61, T.63 Chain D: E.43, T.44, N.46 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain E: N.61, T.63 Chain F: E.43, T.44, N.46 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain C: H.26, N.29, K.32 Chain D: R.248, G.249, T.251, R.333, D.335 Chain F: E.366 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.335, D:D.335 NAG-NAG-BMA-MAN-MAN.8: 8 residues within 4Å: Chain E: H.26, N.29, K.32 Chain F: G.249, T.251, K.252, R.333, D.335 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.252, F:D.335, F:D.335

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.10: 3 residues within 4Å: Chain A: N.67 Chain B: C.83, D.84 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain C: N.67, R.70 Chain D: C.83 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.70 NAG.12: 2 residues within 4Å: Chain E: N.66, N.67 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.66, E:N.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zyla, D.S. et al., A neutralizing antibody prevents postfusion transition of measles virus fusion protein. Science (2024)

Release Date

2024-07-03

Peptides

Fusion glycoprotein F0: ACE
Fusion glycoprotein F0: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
F

B
C

D
E

F
G

Fusion glycoprotein F0

Fusion glycoprotein F0

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