SMTL ID : 7lx3.1

Cryo-EM structure of EDC-crosslinked ConSOSL.UFO.664 (ConS-EDC) in complex with bNAb PGT122

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

33 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: 4 residues within 4Å: Chain A: E.94, N.95, G.534, S.535 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.137, S.194 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: V.184, R.197, I.199, N.202, T.203 Chain D: R.313 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.199 NAG-NAG.4: 2 residues within 4Å: Chain A: N.281, T.283 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.306, I.327, K.441 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: T.375, T.376, N.389, S.391 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: P.366, N.395 Ligands: NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.267, S.296, N.447 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: N.300, N.336, S.338, R.443 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain A: N.239, T.241, P.243, I.277, S.279, H.356 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain A: E.90, V.92, N.234, N.246, S.248 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.90, A:V.92 NAG-NAG.15: 3 residues within 4Å: Chain D: E.94, N.95, S.535 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain D: N.137, S.194 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain D: V.184, R.197, I.199, N.202, T.203 Chain G: R.313 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.184, D:I.199 NAG-NAG.18: 2 residues within 4Å: Chain D: N.281, T.283 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain D: N.306, I.327, K.441 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain D: T.375, T.376, N.389, S.391 Ligands: NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain D: P.366, N.395 Ligands: NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain D: N.267, S.296, N.447 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.20 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain D: N.300, N.336, S.338, R.443 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain D: N.239, T.241, P.243, I.277, S.279, H.356 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain D: E.90, V.92, N.234, N.246, S.248 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.90, D:V.92 NAG-NAG.29: 3 residues within 4Å: Chain G: E.94, N.95, S.535 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain G: N.137, S.194 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 6 residues within 4Å: Chain A: R.313 Chain G: V.184, R.197, I.199, N.202, T.203 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:I.199 NAG-NAG.32: 2 residues within 4Å: Chain G: N.281, T.283 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain G: N.306, I.327, K.441 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain G: T.375, T.376, N.389, S.391 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain G: P.366, N.395 Ligands: NAG-NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 4 residues within 4Å: Chain G: N.267, S.296, N.447 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.34 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain G: N.300, N.336, I.337, S.338, R.443 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 6 residues within 4Å: Chain G: N.239, T.241, P.243, I.277, S.279, H.356 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 5 residues within 4Å: Chain G: E.90, V.92, N.234, N.246, S.248 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:E.90, G:V.92

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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-MAN.6: 8 residues within 4Å: Chain A: L.266, N.267, R.309, G.382, C.444, V.445, S.446 Ligands: NAG-NAG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.382, A:V.445 NAG-NAG-BMA-MAN-MAN-MAN.20: 8 residues within 4Å: Chain D: L.266, N.267, R.309, G.382, C.444, V.445, S.446 Ligands: NAG-NAG.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.382, D:V.445 NAG-NAG-BMA-MAN-MAN-MAN.34: 9 residues within 4Å: Chain G: L.266, N.267, R.309, N.380, G.382, C.444, V.445, S.446 Ligands: NAG-NAG.37 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.382, G:V.445

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN.11: 15 residues within 4Å: Chain A: N.300, T.302, H.334, N.336 Chain B: S.24, N.44, N.45, N.46, P.60, G.61 Chain C: R.103, I.104, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.108 Hydrogen bonds: C:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.25: 15 residues within 4Å: Chain D: N.300, T.302, H.334, N.336 Chain E: S.24, N.44, N.45, N.46, P.60, G.61 Chain F: R.103, I.104, G.106, V.107, V.108 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:V.108 Hydrogen bonds: F:V.108, D:R.331, D:R.331 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.39: 16 residues within 4Å: Chain G: N.300, T.302, H.334, N.336 Chain H: N.44, N.45, N.46, P.60, G.61, S.62 Chain I: R.102, R.103, I.104, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:V.108 Hydrogen bonds: I:V.108, I:R.102, I:R.102

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.14: 13 residues within 4Å: Chain A: N.145 Chain B: D.89, T.94 Chain C: Y.33, H.52, S.54, G.55, D.56, N.58, H.100, R.102, F.114, T.115 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.50, C:N.58 NAG-NAG-BMA-MAN-MAN-MAN.28: 14 residues within 4Å: Chain D: N.145 Chain E: W.88, D.89, R.92, T.94 Chain F: Y.33, S.54, G.55, D.56, N.58, H.100, R.102, F.114, T.115 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.58 NAG-NAG-BMA-MAN-MAN-MAN.42: 15 residues within 4Å: Chain G: N.145 Chain H: W.88, D.89, R.92, T.94 Chain I: Y.33, H.52, S.54, G.55, D.56, N.58, H.100, R.102, F.114, T.115 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.58

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

NAG.43: 3 residues within 4Å: Chain A: N.137, S.160, N.162 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: N.195, Y.196 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain A: E.273, E.274, N.294, Q.348 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: G.339, N.343, W.398 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain A: P.603, W.604, N.605 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: N.137, S.160, N.162 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.195, Y.196 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain D: E.273, E.274, N.294, Q.348 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain D: G.339, N.343, W.398 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain D: P.603, W.604, N.605 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: N.137, S.160, N.162 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: N.195, Y.196 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain G: E.273, E.274, N.294, E.295, Q.348 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain G: N.343, W.398 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain G: P.603, W.604, N.605 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin, G.M. et al., Profound structural conservation of chemically cross-linked HIV-1 envelope glycoprotein experimental vaccine antigens. Npj Vaccines (2023)

Release Date

2022-03-09

Peptides

Env glycoprotein gp160: ADG
PGT122 Fab light chain: BEH
PGT122 Fab heavy chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
L

E
M

H
O

C
H

F
N

I
P

Env glycoprotein gp160

PGT122 Fab light chain

PGT122 Fab heavy chain

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