SMTL ID : 7llk.1

Cryo-EM structure of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

4 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: 3 residues within 4Å: Chain A: D.57, N.58 Chain B: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: V.144, I.157, N.160, T.161 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain E: V.144, N.160, T.161 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain I: V.144, I.157, N.160, T.161 No protein-ligand interaction detected (PLIP)

22 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: 4 residues within 4Å: Chain I: D.57, N.58 Chain J: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: T.98, H.100, S.120, F.121, N.122, K.133, S.152 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: H.55, K.192, D.193, E.194, N.204, K.231 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 7 residues within 4Å: Chain A: G.195, F.196, N.197, T.199, G.200, L.201, Y.314 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: G.350, N.353 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 8 residues within 4Å: Chain A: N.264, N.265, T.266, P.401, G.402, V.403 Chain K: D.69, K.85 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:K.85 NAG-NAG-BMA.9: 9 residues within 4Å: Chain A: H.100, C.101, T.102, N.118, C.119, S.120, K.133, Y.135, D.283 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 11 residues within 4Å: Chain A: T.319, I.321, T.355, Y.357, N.426 Chain D: E.28, S.30, S.31, G.69 Ligands: NAG-NAG-BMA.6, NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain E: H.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 6 residues within 4Å: Chain E: H.55, K.192, D.193, E.194, N.204, K.231 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain E: G.195, F.196, N.197, T.199, G.200, Y.314 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 3 residues within 4Å: Chain E: G.350, N.353 Ligands: NAG-NAG-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 8 residues within 4Å: Chain C: R.67, K.85 Chain E: N.264, N.265, T.266, P.401, G.402, V.403 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.85 NAG-NAG-BMA.19: 7 residues within 4Å: Chain E: C.101, T.102, N.118, C.119, S.120, Y.135, D.283 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 11 residues within 4Å: Chain E: T.319, I.321, Y.357, N.426 Chain H: S.30, S.31, D.67, G.69, D.70 Ligands: NAG-NAG-BMA.16, NAG-NAG-BMA.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 6 residues within 4Å: Chain I: H.100, S.120, F.121, N.122, R.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 6 residues within 4Å: Chain I: H.55, K.192, D.193, E.194, N.204, K.231 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 7 residues within 4Å: Chain I: G.195, F.196, N.197, T.199, G.200, L.201, Y.314 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 3 residues within 4Å: Chain I: G.350, N.353 Ligands: NAG-NAG-BMA.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 7 residues within 4Å: Chain G: K.85 Chain I: N.264, N.265, T.266, P.401, G.402, V.403 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.85 NAG-NAG-BMA.29: 9 residues within 4Å: Chain I: H.100, C.101, T.102, N.118, C.119, S.120, K.133, Y.135, D.283 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 9 residues within 4Å: Chain I: I.321, V.425, N.426 Chain L: E.28, S.30, D.67, G.69, D.70 Ligands: NAG-NAG-BMA.26 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.69

6 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.7: 12 residues within 4Å: Chain A: E.174, P.175, N.225, N.338, C.339, G.340, K.405, C.406, E.407, S.408, N.409 Ligands: NAG.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.340, A:K.405 NAG-NAG-BMA-MAN.12: 10 residues within 4Å: Chain A: E.238, N.239, T.241, N.242 Chain C: E.31, W.32, N.54, W.102, R.103, Y.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.103, C:E.31, C:N.54 NAG-NAG-BMA-MAN.17: 13 residues within 4Å: Chain E: E.174, P.175, K.215, N.225, N.338, C.339, G.340, K.405, C.406, E.407, S.408, N.409 Ligands: NAG.38 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.405 NAG-NAG-BMA-MAN.22: 11 residues within 4Å: Chain E: E.238, N.239, T.241, N.242 Chain G: E.31, W.32, N.54, R.98, W.102, R.103, Y.104 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.103, G:E.31, G:N.54 NAG-NAG-BMA-MAN.27: 14 residues within 4Å: Chain I: E.174, P.175, K.215, V.217, N.225, N.338, C.339, G.340, K.405, C.406, E.407, S.408, N.409 Ligands: NAG.42 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.340, I:K.405 NAG-NAG-BMA-MAN.32: 11 residues within 4Å: Chain I: E.238, N.239, T.241, N.242 Chain K: E.31, W.32, N.54, R.98, W.102, R.103, Y.104 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.103

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

NAG.33: 3 residues within 4Å: Chain A: T.102, N.103, V.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.103, A:N.103, A:N.103 NAG.34: 7 residues within 4Å: Chain A: N.324, S.325, S.326, N.347, S.349, R.430 Chain C: R.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.326, A:S.349 NAG.35: 7 residues within 4Å: Chain A: S.227, L.228, P.254, T.256, E.407, N.409 Ligands: NAG-NAG-BMA-MAN.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.256 Hydrogen bonds: A:N.409 NAG.36: 3 residues within 4Å: Chain E: T.102, N.103, V.104 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.103, E:N.103, E:N.103 NAG.37: 7 residues within 4Å: Chain E: N.324, S.325, S.326, N.347, S.349, R.430 Chain G: R.111 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.326, E:S.349 NAG.38: 7 residues within 4Å: Chain E: S.227, L.228, P.254, T.256, E.407, N.409 Ligands: NAG-NAG-BMA-MAN.17 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.256 Hydrogen bonds: E:N.409 NAG.39: 5 residues within 4Å: Chain E: D.57, N.58 Chain F: A.14, G.16, S.17 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.57 NAG.40: 3 residues within 4Å: Chain I: T.102, N.103, V.104 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:N.103, I:N.103, I:N.103 NAG.41: 7 residues within 4Å: Chain I: N.324, S.325, S.326, N.347, S.349, R.430 Chain K: R.111 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.326, I:S.349 NAG.42: 7 residues within 4Å: Chain I: S.227, L.228, P.254, T.256, E.407, N.409 Ligands: NAG-NAG-BMA-MAN.27 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:T.256 Hydrogen bonds: I:N.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, C.A. et al., Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies. Cell Rep (2021)

Release Date

2021-06-02

Peptides

Envelope glycoprotein gp120: AEI
Envelope glycoprotein gp41: BFJ
179NC75 Fab Heavy chain: CGK
179NC75 Fab Light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

E
A

I
I

B
F

F
B

J
J

C
G

G
C

K
K

D
H

H
D

L
L

Envelope glycoprotein gp120

Envelope glycoprotein gp41

179NC75 Fab Heavy chain

179NC75 Fab Light chain

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