SMTL ID : 5wb0.1

Crystal structure of human metapneumovirus fusion glycoprotein stabilized in the prefusion state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.172, S.192 Chain B: P.64 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.172, S.192 Chain C: P.64 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain A: P.64 Chain C: N.172, S.192 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.2: 4 residues within 4Å: Chain A: E.349, I.352, N.353, T.356 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.9: 4 residues within 4Å: Chain B: E.349, I.352, N.353, T.356 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.349 NAG-NAG-BMA-MAN.16: 4 residues within 4Å: Chain C: E.349, I.352, N.353, T.356 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.349

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

NAG.3: 3 residues within 4Å: Chain A: D.54, E.56, N.57 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.56 Hydrogen bonds: A:E.56 NAG.10: 3 residues within 4Å: Chain B: D.54, E.56, N.57 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.56 Hydrogen bonds: B:E.56, B:E.56 NAG.17: 3 residues within 4Å: Chain C: D.54, E.56, N.57 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.56 Hydrogen bonds: C:E.56, C:E.56

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

SO4.4: 8 residues within 4Å: Chain A: G.366, R.367, H.368, D.454 Chain B: F.103, K.362, A.459, Q.462 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.459, B:Q.462, A:R.367, A:H.368, A:D.454 Salt bridges: B:K.362, A:H.368 SO4.5: 6 residues within 4Å: Chain A: R.329, G.330, D.331, H.332 Chain B: Q.88, L.89 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:L.89, A:D.331, A:D.331, A:H.332 Salt bridges: A:H.332 SO4.6: 2 residues within 4Å: Chain A: R.253, K.324 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.253 SO4.7: 2 residues within 4Å: Chain A: H.435, V.436 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.436 Salt bridges: A:H.435 SO4.11: 8 residues within 4Å: Chain B: G.366, R.367, H.368, D.454 Chain C: F.103, K.362, A.459, Q.462 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.367, B:H.368, B:D.454, C:A.459, C:Q.462 Salt bridges: B:H.368, C:K.362 SO4.12: 6 residues within 4Å: Chain B: R.329, G.330, D.331, H.332 Chain C: Q.88, L.89 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:L.89, B:D.331, B:D.331, B:H.332 Salt bridges: B:H.332 SO4.13: 2 residues within 4Å: Chain B: R.253, K.324 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.253 SO4.14: 2 residues within 4Å: Chain B: H.435, V.436 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.436 Water bridges: B:H.435 Salt bridges: B:H.435 SO4.18: 8 residues within 4Å: Chain A: F.103, K.362, A.459, Q.462 Chain C: G.366, R.367, H.368, D.454 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:F.103, A:A.459, A:Q.462, C:R.367, C:H.368, C:D.454 Salt bridges: A:K.362, C:H.368 SO4.19: 6 residues within 4Å: Chain A: Q.88, L.89 Chain C: R.329, G.330, D.331, H.332 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.331, C:D.331, C:H.332, A:L.89 Salt bridges: C:H.332 SO4.20: 2 residues within 4Å: Chain C: R.253, K.324 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.253 SO4.21: 2 residues within 4Å: Chain C: H.435, V.436 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.436 Salt bridges: C:H.435

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battles, M.B. et al., Structure and immunogenicity of pre-fusion-stabilized human metapneumovirus F glycoprotein. Nat Commun (2017)

Release Date

2017-11-22

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0