SMTL ID : 7n28.1

Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in complex with HIV-1 Env

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-1-1-3-mer

Ligands

25 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: 7 residues within 4Å: Chain A: V.104, T.105, L.106, N.127, S.129, Y.144, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: V.97, T.98, N.131, K.140, K.142 Chain E: D.138 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: R.162, N.167 Chain B: H.73, A.74 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: E.263, N.265, T.267, Y.299, K.405, N.407, V.409 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.405 NAG-NAG.8: 2 residues within 4Å: Chain A: S.261, N.411 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: N.58 Chain M: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: N.303, T.305, K.306, E.309, D.374, I.376 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: Y.55, N.199, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: E.239, I.240, N.259 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain L: N.114 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain D: N.127, Y.144, G.289, D.290 Chain J: D.104, F.105 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:D.104 NAG-NAG.15: 5 residues within 4Å: Chain A: E.135 Chain D: V.153, R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain D: N.265, Y.299, E.301, K.405 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain D: M.341, N.354, T.356 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain D: E.57, N.58 Chain L: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain D: N.303, T.305, K.306 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain D: E.239, I.240, N.259, K.260, Q.313 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain E: N.127, S.129, Y.144, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 6 residues within 4Å: Chain E: F.115, N.265, Y.299, E.301, K.405, N.407 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain E: M.341, N.354, T.356 Ligands: NAG.61 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain E: N.232, S.261, E.263, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain E: E.57, N.58 Chain N: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain E: N.303, T.305, K.306, D.374 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain E: Y.55, N.199, K.201, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 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: 16 residues within 4Å: Chain A: A.35, P.176, K.177, I.178, S.179, D.181, P.182, V.224, N.232, R.274, N.345, R.347, R.403, V.409 Chain F: S.25, D.79 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.409 Hydrogen bonds: A:D.181

2 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.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.62, C:R.62 NAG-NAG-BMA-MAN-MAN-MAN-MAN.17: 12 residues within 4Å: Chain D: E.245, N.246, L.247 Chain G: N.26, G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 Ligands: NAG.47 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.62, G:Y.67

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: 3 residues within 4Å: Chain A: M.341, N.354, T.356 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.16: 9 residues within 4Å: Chain D: D.181, V.224, N.232, N.345, R.347, V.409, S.410 Ligands: NAG.50, MAN.66 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.409

1 x NAG- NAG- BMA- MAN- MAN- MAN: 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.23: 14 residues within 4Å: Chain A: D.138 Chain D: T.98, N.131, D.138, K.140 Chain J: N.30, D.31, R.54, W.76, P.101, E.102, Y.107, Y.108 Ligands: MAN.68 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:D.31, J:R.54, J:E.102, J:Y.108, J:Y.108, J:R.54, J:R.54

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.25: 10 residues within 4Å: Chain B: Q.1 Chain E: I.178, D.181, P.182, V.224, N.232, R.347, V.409, S.410 Ligands: NAG-NAG.29 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.409 Hydrogen bonds: E:R.347, E:R.347

1 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.26: 10 residues within 4Å: Chain E: N.246, T.248 Chain I: N.26, G.27, Y.28, R.62, W.63, G.64, Y.87 Ligands: NAG.59 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.62

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

NAG.34: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.204, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.271, I.292 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.360 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.120, T.122 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: P.323, N.324 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: E.371, N.373 Ligand excluded by PLIP NAG.41: 7 residues within 4Å: Chain A: G.304, T.305, N.308, S.361, K.370, Y.372, T.375 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain C: T.20, R.61, W.63, E.66, N.68 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain D: N.103, D.123 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain D: N.204, T.206, S.244, E.245 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.17 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain D: N.271 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: Q.330, N.360 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain D: E.263, N.411 Ligands: NAG-NAG-BMA-MAN.16 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain D: L.106, N.120, T.122 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain D: N.199, N.211 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: 6 residues within 4Å: Chain D: G.304, N.308, K.370, Y.372, T.375, I.377 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain E: N.103, T.122 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain E: N.131, K.142 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain E: V.153, N.167 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain E: N.204, G.205, T.206 Ligands: NAG-NAG-BMA-MAN.26 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain E: N.271, I.292 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain E: Q.330, N.360 Ligands: NAG-NAG.28, NAG-NAG.28 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain E: N.120, T.122, I.295 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain E: N.308, K.370, Y.372 Ligand excluded by PLIP NAG.65: 4 residues within 4Å: Chain G: T.20, R.61, N.68, T.70 Ligand excluded by PLIP NAG.67: 3 residues within 4Å: Chain I: R.61, W.63, N.68 Ligand excluded by PLIP NAG.69: 4 residues within 4Å: Chain L: N.100, T.102, W.103, Q.130 Ligand excluded by PLIP NAG.70: 1 residues within 4Å: Chain L: N.126 Ligand excluded by PLIP NAG.71: 1 residues within 4Å: Chain L: N.105 Ligand excluded by PLIP NAG.72: 4 residues within 4Å: Chain M: N.100, T.102, W.103, Q.130 Ligand excluded by PLIP NAG.73: 2 residues within 4Å: Chain M: N.126, Y.127 Ligand excluded by PLIP NAG.74: 1 residues within 4Å: Chain M: N.114 Ligand excluded by PLIP NAG.75: 1 residues within 4Å: Chain M: N.105 Ligand excluded by PLIP NAG.76: 4 residues within 4Å: Chain N: N.100, T.102, W.103, Q.130 Ligand excluded by PLIP NAG.77: 1 residues within 4Å: Chain N: N.126 Ligand excluded by PLIP NAG.78: 1 residues within 4Å: Chain N: N.114 Ligand excluded by PLIP

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

PO4.42: 2 residues within 4Å: Ligands: PO4.44, PO4.45 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Salt bridges: E:K.87, A:K.91 PO4.44: 2 residues within 4Å: Ligands: PO4.42, PO4.45 No protein-ligand interaction detected (PLIP) PO4.45: 3 residues within 4Å: Chain D: K.91 Ligands: PO4.42, PO4.44 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Salt bridges: E:K.91, D:K.91

2 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.66: 2 residues within 4Å: Chain H: Q.1 Ligands: NAG-NAG-BMA-MAN.16 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.1 MAN.68: 3 residues within 4Å: Chain J: R.54 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.23, NAG-NAG-BMA-MAN-MAN-MAN.23 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:R.54

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

2022-04-06

Peptides

Envelope glycoprotein gp120: ADE
3BNC117 antibody heavy chain: BFH
3BNC117 antibody light chain: CGI
J033 antibody heavy chain: J
J033 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
M

M
B

N
N

Envelope glycoprotein gp120

3BNC117 antibody heavy chain

3BNC117 antibody light chain

J033 antibody heavy chain

J033 antibody light chain

Envelope glycoprotein gp41

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