SMTL ID : 8tgu.1

Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus nivalis lectin chromatography

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: E.54, N.55, S.495 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: Q.97, S.117, F.118, N.119, K.130 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: R.159, N.164, T.165 Chain C: R.275 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.243, T.245 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: Q.260, N.262, R.409, V.411 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.268, I.289, V.407 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain A: N.329, S.330, G.332, T.338, S.354 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: N.358 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: N.229, P.258, N.413 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.164, T.165 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.201, T.203, P.205, S.241 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.243, T.245, N.246 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.245 NAG-NAG.18: 5 residues within 4Å: Chain B: Q.260, N.262, S.300, R.409, V.411 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.411 NAG-NAG.19: 4 residues within 4Å: Chain B: T.264, H.296, N.298, D.377 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain B: K.301, N.305, T.360, W.361 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain B: G.355, N.358 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain B: L.232, P.258, V.411, N.413 Ligands: NAG.45 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.232 NAG-NAG.23: 6 residues within 4Å: Chain C: N.103, N.115, S.117, K.130, Y.132, D.287 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.117, C:K.130 NAG-NAG.24: 4 residues within 4Å: Chain C: Q.97, S.117, F.118, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: V.141, R.159, N.164, T.165 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain C: N.201, T.203, G.204, P.205, S.241 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.243, T.245, N.246 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 6 residues within 4Å: Chain C: Q.260, N.262, N.298, V.299, S.300, R.409 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain C: N.268, T.270, I.289 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain C: T.264, H.296, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 5 residues within 4Å: Chain C: N.352, S.354, R.384 Ligands: NAG.57, NAG.58 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 2 residues within 4Å: Chain C: P.258, N.413 No protein-ligand interaction detected (PLIP)

5 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: 11 residues within 4Å: Chain A: E.178, V.221, L.228, N.229, F.342, N.343, G.345, C.410, V.411, S.412 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain A: T.264, H.296, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain B: V.101, N.115, Y.132, D.287 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain B: Q.97, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 9 residues within 4Å: Chain C: K.32, E.178, L.228, N.229, F.342, N.343, G.345, V.411, S.412 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.345, C:K.32

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

NAG-BMA.16: 3 residues within 4Å: Chain B: E.178 Ligands: NAG.45, NAG.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.178

25 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.34: 3 residues within 4Å: Chain A: N.585, S.587, E.588 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.604 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.100, K.114 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: N.103, N.104 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: N.201, T.203, S.241, H.318 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.305, S.359, W.361 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: K.313, K.317, N.321 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: N.352, S.354 Ligands: NAG-NAG.9, NAG-NAG.10 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.578, S.580 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.585 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: N.100, K.114, R.137 Ligand excluded by PLIP NAG.45: 10 residues within 4Å: Chain B: V.221, L.228, N.229, N.343, C.410, V.411, S.412 Ligands: NAG-BMA.16, NAG-NAG.22, NAG.46 Ligand excluded by PLIP NAG.46: 7 residues within 4Å: Chain B: E.178, G.345, R.409, C.410 Ligands: NAG-BMA.16, NAG-BMA.16, NAG.45 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: N.268, I.289, V.407 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: N.321, N.322 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain B: N.329, S.330, S.331, T.338 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.585, E.588 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain C: K.600, E.601, I.602, S.603, N.604 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.55 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: N.100, R.110, G.111 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain C: Q.142, N.144, K.156 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: K.301, N.305, W.361 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: K.317, N.321 Ligand excluded by PLIP NAG.57: 6 residues within 4Å: Chain C: N.329, S.330, S.331, T.338 Ligands: NAG-NAG.32, NAG-NAG.32 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain C: S.354, N.358 Ligands: NAG-NAG.32 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parthasarathy, D. et al., Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted/founder sensitivity to broadly neutralizing antibodies. Nat Commun (2024)

Release Date

2024-08-28

Peptides

HIV-1 Envelope glycoprotein BG505 SOSIP: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HIV-1 Envelope glycoprotein BG505 SOSIP