SMTL ID : 8tnu.1

Cryo-EM structure of TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

17 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 C: E.123, N.126 Chain F: T.56, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain H: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: R.29, W.105, T.106 Chain C: S.17 Chain H: E.57, N.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.105 NAG-NAG.4: 5 residues within 4Å: Chain H: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain H: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain H: N.265, N.301, V.302, S.303, R.412, V.414 Ligands: NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain H: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain H: P.261, Q.263, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain F: W.105 Chain I: E.57, N.58 Chain L: G.16, S.17 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:W.105 NAG-NAG.11: 3 residues within 4Å: Chain I: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain I: N.106, N.118, Y.135, L.137, D.290 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:Y.135 Hydrogen bonds: I:Y.135, I:Y.135 NAG-NAG.13: 5 residues within 4Å: Chain I: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain J: L.235, P.261, N.416 Ligands: NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain J: N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain J: Q.263, N.265, N.301, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain H: D.129 Chain J: T.98, Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain K: K.122, E.123, S.125, N.126 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.9: 12 residues within 4Å: Chain H: 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.8 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:V.414 NAG-NAG-BMA-MAN-MAN.14: 10 residues within 4Å: Chain I: E.181, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.46 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:V.414 Hydrogen bonds: I:G.348

4 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.15: 3 residues within 4Å: Chain J: E.57, N.58 Chain K: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 9 residues within 4Å: Chain J: E.181, P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.16 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.348 NAG-NAG-BMA.21: 6 residues within 4Å: Chain J: N.106, N.118, S.120, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 3 residues within 4Å: Chain D: N.58 Chain L: E.123, N.126 No protein-ligand interaction detected (PLIP)

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

NAG.24: 3 residues within 4Å: Chain C: N.105, R.106, N.107 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: N.100 Chain F: Y.53 Chain L: A.1, I.4 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain H: N.103, R.113 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain H: N.271, I.292, V.410 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain H: T.267, H.299, N.301, T.383, R.412 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain H: N.308, W.364 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain H: N.324 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain H: N.332, S.333, T.341, S.357 Ligands: NAG.32, NAG.34 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain H: S.357, N.361 Ligands: NAG.31, NAG.34 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain H: R.162, N.167 Chain I: R.278 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain H: T.342, N.355, S.357, R.387 Ligands: NAG.31, NAG.32 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain I: N.103, G.114, K.117, R.140 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain I: R.162, N.167 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain I: N.204, T.206 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain I: N.265, V.302, S.303, R.412 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain I: N.271, I.292, V.410 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain I: T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain I: K.304, N.308 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.43: 7 residues within 4Å: Chain I: N.332, S.333, S.334, G.335, S.357 Ligands: NAG.44, NAG.45 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain I: T.341, N.355, S.357 Ligands: NAG.43 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain I: S.357, N.361 Ligands: NAG.43 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain I: N.232, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.14 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain J: N.103, K.117 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain J: R.162, N.167, T.168 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain J: N.271, I.292, V.410 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain J: T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain J: N.308, W.364 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain J: N.324 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain J: N.332, S.333 Ligands: NAG.54 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain J: N.355, S.357 Ligands: NAG.53, NAG.55 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain J: N.361 Ligands: NAG.54 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain J: N.204, T.206, S.244, I.247 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain K: N.100, S.102 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain K: N.107 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain L: N.107 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain K: A.1, V.2 Chain L: N.100 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques. To Be Published

Release Date

2024-08-07

Peptides

TRNM-b*01 heavy chain: ADF
TRNM-b*01 light chain: BEG
Transmembrane protein gp41: CKL
BG505 DS-SOSIP Surface protein gp120: HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
J

F
H

B
C

E
K

G
L

C
Z

K
X

L
Y

H
G

I
E

J
F

TRNM-b*01 heavy chain

TRNM-b*01 light chain

Transmembrane protein gp41

BG505 DS-SOSIP Surface protein gp120

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