SMTL ID : 9d3d.1

Cryo-EM structure of PGT145 R100aS Fab bound to HIV-1 BG505 DS-SOSIP.664 Env trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

22 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: 6 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.3, NAG-NAG.3, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.332, T.341 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain A: N.232, L.235, P.261, V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.34 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 7 residues within 4Å: Chain B: Q.263, N.265, N.301, V.302, S.303, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain B: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain B: N.355, S.357 Ligands: NAG-NAG.15, NAG-NAG.15, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.361 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain B: T.267, H.299, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.24, NAG-NAG.24, NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 7 residues within 4Å: Chain C: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.23, NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain B: R.278 Chain C: V.144, R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain C: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.103, G.114, R.140 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain C: N.107, G.293 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 6 residues within 4Å: Chain C: L.235, P.261, Q.263, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.36 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.4: 6 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 Chain G: D.56, T.58 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:D.56 Hydrogen bonds: G:D.56, G:T.58 NAG-NAG-BMA-MAN-MAN.26: 13 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.131 Chain G: D.106, Y.107, E.119, Y.123 Chain H: L.29, Q.30, H.31, S.32 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.106, G:D.106, G:Y.123

2 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.5: 5 residues within 4Å: Chain A: N.106, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.30: 5 residues within 4Å: Chain C: N.106, N.118, S.120, Y.135, D.290 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.8: 2 residues within 4Å: Chain A: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain B: N.106, N.118, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 6 residues within 4Å: Chain B: L.235, P.261, V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain B: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP)

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.11: 10 residues within 4Å: Chain B: E.181, L.231, N.232, F.345, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.348, B:V.414 NAG-NAG-BMA-MAN-MAN-MAN.34: 10 residues within 4Å: Chain A: E.181, L.231, N.232, N.346, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN-MAN.36: 8 residues within 4Å: Chain C: E.181, L.231, N.232, N.346, C.413, V.414, S.415 Ligands: NAG-NAG.33 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.414

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.13: 13 residues within 4Å: Chain B: Q.100, S.120, F.121, N.122, K.133 Chain G: N.31, H.53, E.54, K.101, H.102, R.103, L.104 Chain H: Y.37 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.103, G:R.103

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.31: 3 residues within 4Å: Chain C: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP)

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

NAG.37: 3 residues within 4Å: Chain A: E.57, N.58 Chain D: S.17 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.103, G.114 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain A: N.107 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: E.57, N.58 Chain E: G.16, S.17 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: N.103, K.117, Y.161 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: N.204, T.206, S.244, I.247 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: N.271, I.292, V.410 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.308 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.324 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain B: N.106, N.107, G.293, D.294 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: E.57, N.58 Chain F: G.16, S.17 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: N.271, I.292, V.410 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain C: K.304, N.308, W.364 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain C: K.316, R.319, K.320, N.324 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain D: N.126 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain E: N.100, S.102 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain E: N.126, Y.127 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain F: N.126 Ligand excluded by PLIP

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

PO4.50: 3 residues within 4Å: Chain A: K.87 Chain B: K.87 Chain C: K.87 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Salt bridges: A:K.87, C:K.87, B:K.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hodges, S. et al., Structural Development of the HIV-1 Apex-Directed PGT145-PGDM1400 Antibody Lineage. Cell Rep (2024)

Release Date

2024-12-25

Peptides

HIV-1 BG505 DS-SOSIP gp120: ABC
BG505 DS-SOSIP glycoprotein gp41: DEF
PGT145 R100aS Heavy Chain: G
PGT145 Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
c

E
a

F
b

G
H

H
L

HIV-1 BG505 DS-SOSIP gp120

BG505 DS-SOSIP glycoprotein gp41

PGT145 R100aS Heavy Chain

PGT145 Light Chain

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