SMTL ID : 7jpi.1

Crystal structure of EBOV glycoprotein with modified HR2 stalk at 2.3A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-3-3-mer

Ligands

6 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: 1 residues within 4Å: Chain A: N.238 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: T.217, N.257, Y.261 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain C: N.238 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: T.217, N.257, Y.261 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain E: N.238 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: T.217, N.257, Y.261 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.3: 11 residues within 4Å: Chain A: L.70, E.156, G.157, A.158, V.180 Chain B: Q.7, P.8, N.62, T.65 Chain D: L.28, F.34 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.8 Water bridges: A:K.155 NAG-NAG-BMA-MAN-MAN-MAN.10: 11 residues within 4Å: Chain C: L.70, E.156, G.157, A.158, V.180 Chain D: Q.7, P.8, N.62, T.65 Chain F: L.28, F.34 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.8 Water bridges: C:K.155 NAG-NAG-BMA-MAN-MAN-MAN.17: 11 residues within 4Å: Chain B: L.28, F.34 Chain E: L.70, E.156, G.157, A.158, V.180 Chain F: Q.7, P.8, N.62, T.65 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Water bridges: E:K.155 Hydrophobic interactions: F:P.8

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.120, L.122, P.123, D.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.120, A:D.150, A:R.172 GOL.5: 3 residues within 4Å: Chain A: R.89 Chain D: F.34, G.35 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.89, D:F.34 Water bridges: A:R.89, A:R.89 GOL.11: 4 residues within 4Å: Chain C: E.120, L.122, P.123, D.150 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.120, C:D.150, C:R.172 GOL.12: 3 residues within 4Å: Chain C: R.89 Chain F: F.34, G.35 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:R.89, F:F.34 Water bridges: C:R.89, C:R.89 GOL.18: 4 residues within 4Å: Chain E: E.120, L.122, P.123, D.150 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.120, E:D.150, E:R.172 GOL.19: 3 residues within 4Å: Chain B: F.34, G.35 Chain E: R.89 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:F.34, E:R.89 Water bridges: E:R.89, E:R.89

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

NAG.6: 2 residues within 4Å: Chain A: G.264, N.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.268 NAG.13: 2 residues within 4Å: Chain C: G.264, N.268 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.268 NAG.20: 2 residues within 4Å: Chain E: G.264, N.268 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.268

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 4 residues within 4Å: Chain A: I.33 Chain B: R.86, K.87, D.90 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.90, A:I.33 Salt bridges: B:R.86, B:K.87 PO4.14: 4 residues within 4Å: Chain C: I.33 Chain D: R.86, K.87, D.90 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:I.33, D:D.90 Salt bridges: D:R.86, D:K.87 PO4.21: 4 residues within 4Å: Chain E: I.33 Chain F: R.86, K.87, D.90 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:D.90, E:I.33 Salt bridges: F:R.86, F:K.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, L. et al., Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines. Nat Commun (2021)

Release Date

2021-04-07

Peptides

Envelope glycoprotein: ACE
Envelope glycoprotein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Envelope glycoprotein

Envelope glycoprotein