SMTL ID : 7tcn.1

Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.10 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

6 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.1: 6 residues within 4Å: Chain I: D.196, N.247, N.360, G.362, I.429, N.431 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.362 NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: K.237, L.246, N.247, N.360, C.428, I.429, S.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.429 NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: T.355, T.356, N.369, S.371, R.402 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 5 residues within 4Å: Chain E: T.355, T.356, N.369, S.371, R.402 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 6 residues within 4Å: Chain E: D.196, K.237, N.247, N.360, G.362, I.429 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.362 NAG-NAG-BMA.10: 6 residues within 4Å: Chain I: T.355, T.356, N.369, S.371, R.402 Ligands: NAG.26 No protein-ligand interaction detected (PLIP)

3 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.2: 11 residues within 4Å: Chain I: V.167, R.177, N.182, T.183 Chain K: T.19, Y.71, D.73, S.75, M.76, Y.80 Ligands: MAN.27 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.73 NAG-NAG-BMA-MAN.5: 11 residues within 4Å: Chain A: V.167, R.177, N.182, T.183 Chain C: T.19, Y.71, D.73, S.75, M.76, Y.80 Ligands: MAN.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.73 NAG-NAG-BMA-MAN.9: 11 residues within 4Å: Chain E: V.167, R.177, N.182, T.183 Chain G: T.19, Y.71, D.73, S.75, M.76, Y.80 Ligands: MAN.22 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.73

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

NAG-NAG.7: 4 residues within 4Å: Chain E: E.319, N.323, R.376, R.395 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.395 NAG-NAG.11: 5 residues within 4Å: Chain I: E.319, N.323, Q.327, R.376, R.395 No protein-ligand interaction detected (PLIP)

13 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.12: 4 residues within 4Å: Chain A: E.319, N.323, R.376, R.395 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.376, A:R.395 NAG.13: 4 residues within 4Å: Chain A: N.124, S.143, F.144, N.145 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.124 Hydrogen bonds: A:N.145 NAG.14: 2 residues within 4Å: Chain A: N.215, T.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.215, A:T.217 NAG.15: 3 residues within 4Å: Chain A: V.79, N.214, N.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.214, A:N.226 NAG.16: 4 residues within 4Å: Chain A: P.346, S.371, N.375 Ligands: NAG-NAG-BMA.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.346 NAG.18: 4 residues within 4Å: Chain E: N.124, S.143, F.144, N.145 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.145, E:N.145 NAG.19: 3 residues within 4Å: Chain E: V.79, N.214, N.226 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.214, E:N.226 NAG.20: 3 residues within 4Å: Chain E: N.215, T.217, N.225 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.215, E:T.217, E:N.225, E:N.225 NAG.21: 3 residues within 4Å: Chain E: P.346, S.371, N.375 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.346 NAG.23: 4 residues within 4Å: Chain I: N.124, S.143, F.144, N.145 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.145, I:N.145 NAG.24: 3 residues within 4Å: Chain I: N.215, T.217, N.225 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.215, I:N.225 NAG.25: 3 residues within 4Å: Chain I: V.79, N.214, N.226 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.214, I:N.226 NAG.26: 3 residues within 4Å: Chain I: P.346, N.375 Ligands: NAG-NAG-BMA.10 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:P.346

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

MAN.17: 3 residues within 4Å: Chain C: Y.71 Ligands: NAG-NAG-BMA-MAN.5, NAG-NAG-BMA-MAN.5 No protein-ligand interaction detected (PLIP) MAN.22: 4 residues within 4Å: Chain G: Y.71, R.72 Ligands: NAG-NAG-BMA-MAN.9, NAG-NAG-BMA-MAN.9 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.351, E:D.351 MAN.27: 4 residues within 4Å: Chain I: D.351 Chain K: Y.71 Ligands: NAG-NAG-BMA-MAN.2, NAG-NAG-BMA-MAN.2 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.351, I:D.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manne, K., Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.G458Y.SOSIP.664. To Be Published

Release Date

2023-08-02

Peptides

Envelope glycoprotein gp160: AEI
Glycoprotein 41: BFJ
CH235.12 Fab Heavy Chain: CGK
CH235.12 Fab Light Chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

Envelope glycoprotein gp160

Glycoprotein 41

CH235.12 Fab Heavy Chain

CH235.12 Fab Light Chain

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