SMTL ID : 9btl.1

Cryo-EM structure of rhesus antibody 41328-a.01 in complex with HIV-1 Env BG505 DS-SOSIP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

27 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: N.332, S.333, T.341, N.355 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.1, NAG-NAG.1, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: R.162, N.167, T.168 Chain F: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain C: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.13, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG.13, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.11, NAG-NAG.11, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain C: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain A: R.278 Chain C: V.144, R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain C: N.232, L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.204, T.206, S.244, E.245 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain F: N.332, S.333, T.341 Ligands: NAG-NAG.26, NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain F: S.357, N.361 Ligands: NAG-NAG.26, NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG.24, NAG-NAG.24, NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain F: Q.263, N.265, S.303, R.412 Ligands: NAG-NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 5 residues within 4Å: Chain C: R.278 Chain F: V.144, R.162, I.164, N.167 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.144 NAG-NAG.32: 4 residues within 4Å: Chain F: N.103, G.114, K.117, R.140 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 7 residues within 4Å: Chain F: T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain F: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain F: N.204, T.206, S.244, E.245 No protein-ligand interaction detected (PLIP)

4 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.4: 11 residues within 4Å: Chain A: E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, V.414, S.415 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN.14: 12 residues within 4Å: Chain C: S.179, E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.181, C:S.179 NAG-NAG-BMA-MAN.29: 8 residues within 4Å: Chain E: Q.1, Y.33, E.105 Chain F: Q.100, S.120, F.121, N.122, K.133 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.1, E:Y.33 NAG-NAG-BMA-MAN.30: 5 residues within 4Å: Chain F: N.106, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP)

2 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.7: 5 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 11 residues within 4Å: Chain F: E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, V.414, S.415 Ligands: NAG.52 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.348, F:V.414

1 x NAG- NAG- BMA- MAN: 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.16: 14 residues within 4Å: Chain C: T.98, Q.100, S.120, F.121, N.122 Chain E: Y.104, D.106, Y.112, Y.117 Chain H: S.33, H.51, N.52, G.53, Q.54 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:Y.117, H:H.51 Hydrogen bonds: H:N.52, H:Q.54, H:Q.54

1 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.17: 12 residues within 4Å: Chain C: V.104, N.118, Y.135, L.137, G.289, D.290 Chain E: N.60, K.66 Chain H: S.27, D.94, M.95, N.97 4 PLIP interactions: 1 interactions with chain H, 1 interactions with chain C, 2 interactions with chain E Hydrogen bonds: H:D.94, C:D.290, E:N.60, E:N.60

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

NAG.36: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.4 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: N.103, K.117, R.140 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: E.57, N.58 Chain B: S.16 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: N.204, T.206, S.244 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: N.246, T.248 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: N.106, N.107, G.293 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: K.121, E.122, S.124, N.125 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.246, T.248, N.249 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.103 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: N.308, L.311, S.362, W.364 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.107 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain D: N.99, S.101, W.102 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain D: K.121, E.122, N.125, Y.126 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain F: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.27 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain F: N.246, T.248, N.249 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain F: N.324 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain F: E.57, N.58 Chain G: S.16 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain F: N.308 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain F: N.107, D.294 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain G: N.104, N.106, S.108, E.109 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain G: K.121, E.122, N.125 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roark, R.S. et al., Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies. J.Exp.Med. (2025)

Release Date

2025-05-21

Peptides

Envelope glycoprotein Gp120: ACF
Envelope glycoprotein Gp41: BDG
41328-a.01 heavy chain: E
41328-a.01 light chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
E

F
I

B
B

D
F

G
J

E
H

H
L

Envelope glycoprotein Gp120

Envelope glycoprotein Gp41

41328-a.01 heavy chain

41328-a.01 light chain

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