SMTL ID : 9bnp.1

Cryo-EM structure of rhesus antibody V033-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

29 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.327, S.328, T.336, N.350 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.356 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.350, S.352 Ligands: NAG-NAG.1, NAG-NAG.1, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.241, T.243, N.244 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: K.315, N.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.315 NAG-NAG.7: 4 residues within 4Å: Chain A: Q.258, N.260, S.298, R.407 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: Q.98, S.115, F.116, N.117, K.128 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: V.102, N.104, N.113, Y.130, D.285 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: V.139, R.157, I.159, N.162 Chain F: R.273 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain A: T.262, H.294, N.296, S.376, T.378, R.407 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain C: N.327, S.328, T.336, N.350, S.352 Ligands: NAG-NAG.14, NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: G.353, N.356 Ligands: NAG-NAG.14, NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: N.350, S.352 Ligands: NAG-NAG.12, NAG-NAG.12, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.241, T.243, N.244 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.243 NAG-NAG.17: 6 residues within 4Å: Chain C: Q.258, N.260, N.296, S.298, R.407 Ligands: NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain A: R.273 Chain C: V.139, R.157, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: E.55, N.56 Chain D: S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain C: T.262, H.294, N.296, T.378 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: N.266, I.287, V.405 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain C: N.227, L.230, P.256, N.411 Ligands: NAG-NAG-BMA-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 7 residues within 4Å: Chain F: N.327, S.328, T.336, N.350, S.352 Ligands: NAG-NAG.27, NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain F: S.352, G.353, N.356 Ligands: NAG-NAG.27, NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain F: N.350, S.352 Ligands: NAG-NAG.25, NAG-NAG.25, NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 7 residues within 4Å: Chain F: Q.258, N.260, N.296, V.297, S.298, R.407 Ligands: NAG-NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain C: R.273 Chain F: R.157, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain F: N.101, K.112, R.135 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 6 residues within 4Å: Chain F: T.262, H.294, N.296, S.376, R.407 Ligands: NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 2 residues within 4Å: Chain F: N.266, I.287 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain F: N.199, T.201, S.239 No protein-ligand interaction detected (PLIP)

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.4: 13 residues within 4Å: Chain A: S.174, E.176, P.177, V.219, L.226, N.227, N.341, C.342, G.343, C.408, V.409, S.410 Ligands: NAG.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.343 NAG-NAG-BMA-MAN.15: 10 residues within 4Å: Chain C: S.174, E.176, P.177, L.226, N.227, N.341, C.408, V.409, S.410 Ligands: NAG-NAG.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.176

1 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.18: 15 residues within 4Å: Chain C: Q.98, S.115, F.116, N.117, K.128 Chain E: N.52, G.54, G.56, S.71, R.72, D.73, N.74, S.75, T.109, V.110 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.110 Hydrogen bonds: E:N.52, E:G.56, E:S.71

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.19: 15 residues within 4Å: Chain C: V.102, N.104, N.113, Y.130, L.132, D.285 Chain E: E.1, G.26, D.31, D.100, G.101, D.102, Y.104, K.120 Chain H: E.55 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: C:Y.130 Hydrogen bonds: E:Y.118, E:K.120, H:E.55

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.28: 11 residues within 4Å: Chain F: E.176, P.177, L.226, N.227, N.341, C.342, G.343, C.408, V.409, S.410 Ligands: NAG.48 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.343, F:V.409 NAG-NAG-BMA.31: 4 residues within 4Å: Chain F: V.102, N.113, Y.130, D.285 No protein-ligand interaction detected (PLIP)

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.30: 11 residues within 4Å: Chain E: Y.57, D.113, K.116 Chain F: Q.98, S.115, F.116, N.117, K.128 Chain H: Y.92, S.93, A.94 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain E Hydrogen bonds: H:Y.92, E:Y.57, E:K.116

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

NAG.37: 5 residues within 4Å: Chain A: N.227, P.256, Q.258, N.411 Ligands: NAG-NAG-BMA-MAN.4 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: T.100, N.101 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: E.55, N.56 Chain B: S.9 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.303 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: P.264, N.266, I.287, G.288 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain A: N.199, T.201, S.239, E.240 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.319 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.101 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.303, S.357 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.199, T.201, S.239, I.242 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: N.92, S.94 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain F: N.227, P.256, N.411 Ligands: NAG-NAG-BMA.28 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain F: N.241, T.243, N.244 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain F: N.319 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain F: E.55, N.56 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain F: K.299, N.303, W.359 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain G: N.118, Y.119 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain G: N.97, R.98, N.99, S.101, E.102 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

2025-05-07

Peptides

Envelope glycoprotein Gp120: ACF
Envelope glycoprotein Gp41: BDG
V033-a.01 heavy chain: E
V033-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

V033-a.01 heavy chain

V033-a.01 light chain

Related Entries With Identical Sequence