SMTL ID : 7mxd.1

Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 Env

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-1-1-3-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: V.104, T.105, N.127, S.129, Y.144, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: T.98, S.129, N.131 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: V.153, R.162, I.164, N.167 Chain B: H.73 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: E.263, N.265, Y.299, E.301 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: L.235, S.261, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: E.57, N.58 Chain L: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: N.303, T.305, K.306, D.374 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: N.199, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: E.239, I.240, N.259, Q.313, K.317 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain M: N.114 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain D: V.104, T.105, L.106, N.127, Y.144, L.146, D.290 Chain J: F.105 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: D:Y.144, J:F.105 NAG-NAG.15: 4 residues within 4Å: Chain D: R.162, N.167 Chain F: H.73, W.76 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain D: E.263, N.265, E.301, K.405, N.407, V.409 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain D: T.340, M.341, N.354, T.356 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain D: N.232, S.261, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain D: E.57, N.58 Chain M: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain D: N.303, T.305, K.306, D.374 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain D: Y.55, N.199, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain D: G.238, E.239, I.240, N.259 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain E: V.104, T.105, N.127, L.146 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain E: N.265, T.267, Y.299, E.301 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain E: T.340, M.341, N.354, T.356 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain E: N.232, S.261, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain E: E.57, N.58 Chain N: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain E: N.303, T.305, K.306, D.374 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain E: Y.55, N.199, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain E: E.239, I.240, N.259 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.4: 13 residues within 4Å: Chain A: A.35, K.177, I.178, S.179, D.181, L.231, N.232, N.345, R.347, V.409, S.410 Chain F: Q.1 Ligands: NAG-NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.409

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.5: 10 residues within 4Å: Chain A: E.245, N.246 Chain C: G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 Ligands: NAG.37 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.28 Hydrogen bonds: C:R.62, C:R.62 NAG-NAG-BMA-MAN-MAN-MAN-MAN.17: 10 residues within 4Å: Chain D: E.245, N.246 Chain G: G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 Ligands: NAG.49 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:Y.28 Hydrogen bonds: G:R.62, G:Y.67 NAG-NAG-BMA-MAN-MAN-MAN-MAN.25: 10 residues within 4Å: Chain D: T.98, S.100, S.129, N.131, K.140 Chain J: N.30, R.54, P.101, Y.107, Y.108 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.54, J:Y.108, J:R.54, J:R.54 NAG-NAG-BMA-MAN-MAN-MAN-MAN.28: 11 residues within 4Å: Chain E: E.245, N.246 Chain I: N.26, G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 Ligands: NAG.59 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.28 Hydrogen bonds: I:R.62

1 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: 4 residues within 4Å: Chain A: T.340, M.341, N.354, T.356 No protein-ligand interaction detected (PLIP)

2 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.16: 14 residues within 4Å: Chain D: T.33, A.35, P.176, K.177, I.178, S.179, V.224, N.232, N.345, C.408, V.409, S.410 Chain H: Q.1 Ligands: NAG-NAG.20 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.409 NAG-NAG-BMA-MAN-MAN-MAN.27: 15 residues within 4Å: Chain B: Q.1 Chain E: T.33, A.35, K.177, I.178, S.179, D.181, V.224, L.231, N.232, N.345, R.347, V.409, S.410 Ligands: NAG-NAG.31 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.409

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

NAG.36: 2 residues within 4Å: Chain A: N.103, D.123 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: N.204, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.271, T.273 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: Q.330, P.331, N.360 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: N.120, T.122 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: P.323, N.324 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: E.371, N.373 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain A: T.305, N.308, S.361, Y.372, N.373 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: T.22, R.61, E.66, N.68 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: N.103, D.123 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain D: N.204, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.17 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: N.271, T.273 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain D: Q.330, N.360 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain D: L.106, N.120 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain D: P.323, N.324 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain D: N.373 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain D: N.308, W.363, Y.372, T.375 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain E: S.129, F.130, N.131 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain E: V.153, N.167, T.168 Chain H: H.73, W.76 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain E: N.204, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.28 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain E: N.271, I.292 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain E: Q.330, N.360 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain E: N.108, N.120, T.122 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.64: 4 residues within 4Å: Chain E: N.308, W.363, K.370, Y.372 Ligand excluded by PLIP NAG.65: 4 residues within 4Å: Chain G: T.20, R.61, W.63, N.68 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain I: E.66, N.68 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain L: P.98, N.100, T.102, I.134 Ligand excluded by PLIP NAG.68: 1 residues within 4Å: Chain L: N.126 Ligand excluded by PLIP NAG.69: 1 residues within 4Å: Chain L: N.114 Ligand excluded by PLIP NAG.70: 1 residues within 4Å: Chain L: N.105 Ligand excluded by PLIP NAG.71: 5 residues within 4Å: Chain M: N.100, T.102, W.103, Y.127, Q.130 Ligand excluded by PLIP NAG.72: 2 residues within 4Å: Chain M: E.123, N.126 Ligand excluded by PLIP NAG.73: 1 residues within 4Å: Chain M: N.105 Ligand excluded by PLIP NAG.74: 2 residues within 4Å: Chain N: N.100, T.102 Ligand excluded by PLIP NAG.75: 2 residues within 4Å: Chain N: E.123, N.126 Ligand excluded by PLIP NAG.76: 2 residues within 4Å: Chain N: Q.110, N.114 Ligand excluded by PLIP

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

PO4.44: 3 residues within 4Å: Chain A: K.87 Ligands: PO4.46, PO4.47 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.87, A:K.91 PO4.46: 5 residues within 4Å: Chain D: K.87, K.91, K.172 Ligands: PO4.44, PO4.47 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:K.87, D:K.91, D:K.172 PO4.47: 5 residues within 4Å: Chain A: K.91 Chain D: K.91 Chain E: K.91 Ligands: PO4.44, PO4.46 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 interactions with chain A Salt bridges: E:K.91, D:K.91, A:K.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, N. et al., Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2. Adv Sci (2022)

Release Date

2022-03-30

Peptides

Envelope glycoprotein gp120: ADE
3BNC117 antibody heavy chain: BFH
3BNC117 antibody light chain: CGI
J038 antibody heavy chain: J
J038 antibody light chain: K
Envelope glycoprotein gp41: LMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
F

E
G

B
C

F
J

H
S

C
D

G
K

I
U

J
X

K
Y

L
B

M
I

N
H

Envelope glycoprotein gp120

3BNC117 antibody heavy chain

3BNC117 antibody light chain

J038 antibody heavy chain

J038 antibody light chain

Envelope glycoprotein gp41

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