SMTL ID : 8dp1.1

Cryo-EM structure of HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.1: 24 residues within 4Å: Chain A: R.51, Y.54, E.55, K.58, L.59, D.60, S.61 Chain B: F.32, R.98, P.101, Y.103, R.104, Y.105, W.106, G.109, H.111, D.113, P.114 Chain D: T.267, H.299, N.301, S.381, T.383, R.412 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.105 Hydrogen bonds: B:Y.105 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.6: 21 residues within 4Å: Chain E: T.267, H.299, N.301, S.381, T.383 Chain F: F.32, R.98, P.101, Y.103, Y.105, W.106, G.109, H.111, D.113 Chain G: R.51, Y.54, E.55, K.58, L.59, D.60, S.61 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:Y.105 Hydrogen bonds: F:Y.105, F:W.106 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11: 25 residues within 4Å: Chain I: T.267, H.299, N.301, D.380, S.381, T.383, R.412 Chain J: F.32, R.98, P.101, Y.103, R.104, Y.105, W.106, G.109, H.111, D.113, P.114 Chain K: R.51, Y.54, E.55, K.58, L.59, D.60, S.61 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:Y.105 Hydrogen bonds: J:Y.105

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.2: 7 residues within 4Å: Chain D: E.181, L.231, N.232, N.346, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain D: V.104, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain E: T.105, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 8 residues within 4Å: Chain E: E.181, P.182, L.231, N.232, N.346, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain I: V.104, N.118, Y.135 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 2 residues within 4Å: Chain D: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain D: Q.263, N.265, N.301, V.302, S.303, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain E: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain E: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain I: Q.263, N.265, N.301, V.302, S.303, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain I: N.271, T.273, I.292 No protein-ligand interaction detected (PLIP)

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.15: 9 residues within 4Å: Chain I: K.35, E.181, P.182, L.231, N.232, N.346, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain C: N.100, S.102 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain C: R.106, E.110, N.114, M.115, E.123 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain C: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain D: N.103, D.110, D.111, R.113, G.114 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain D: R.162, N.167, T.168 Chain I: R.278 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain D: N.204, T.206, S.244, I.247 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.246, T.248, N.249 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain D: N.324 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: N.332, S.333, S.357 Ligands: NAG.26 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG.25 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain E: N.103, D.110, D.111, R.113, G.114 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: R.278 Chain E: R.162, N.167 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain E: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: N.246, T.248, N.249 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: N.332, S.333, S.357 Ligands: NAG.34 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG.33 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain H: N.100, S.102 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain H: R.106, E.110, N.114, M.115, E.123 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain H: K.122, E.123, S.125, N.126, Y.127 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain I: N.103, D.110, D.111, R.113 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain I: Q.100, S.120, N.122 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: R.278 Chain I: R.162, N.167 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain I: N.204, T.206, S.244 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain I: N.246, T.248, N.249 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain I: N.332, S.333, S.357 Ligands: NAG.45 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG.44 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain L: N.100, S.102 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain L: R.106, E.110, N.114, M.115, E.123 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain L: K.122, E.123, S.125, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Shared recognition mechanism for HIV-1 envelope-reactive V3 glycan broadly neutralizing B cell lineage maturation in humans and macaques. To Be Published

Release Date

2023-07-19

Peptides

DH1030.1 Fab light chain: AGK
DH1030.1 Fab Heavy chain: BFJ
Envelope glycoprotein gp41: CHL
Envelope glycoprotein gp120: DEI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

G
F

K
O

B
R

F
E

J
N

C
S

H
H

L
Q

D
W

E
B

I
J

DH1030.1 Fab light chain

DH1030.1 Fab Heavy chain

Envelope glycoprotein gp41

Envelope glycoprotein gp120

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