SMTL ID : 7tco.1

Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.G458Y.SOSIP.664 with high-mannose glycans

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.19 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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: 4 residues within 4Å: Chain A: T.330, N.344, S.346, R.377 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain E: T.330, N.344, S.346, R.377 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain I: T.330, N.344, S.346, R.377 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 4 residues within 4Å: Chain A: E.294, S.295, N.298, T.369 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain E: E.294, S.295, N.298, T.369 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain I: E.294, S.295, N.298, T.369 No protein-ligand interaction detected (PLIP)

3 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.3: 11 residues within 4Å: Chain A: R.152, N.157, T.158, G.324, G.325 Chain C: T.19, Y.71, D.73, S.75, M.76, Y.80 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.73 NAG-NAG-BMA-MAN-MAN-MAN.7: 10 residues within 4Å: Chain E: R.152, N.157, T.158, G.324, G.325 Chain G: T.19, Y.71, D.73, S.75, Y.80 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.11: 11 residues within 4Å: Chain I: R.152, N.157, T.158, G.324, G.325 Chain K: T.19, Y.71, D.73, S.75, M.76, Y.80 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.73

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.4: 6 residues within 4Å: Chain A: K.167, L.221, N.222, N.335, I.404, S.405 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.167, A:K.167 NAG-NAG-BMA-MAN.8: 6 residues within 4Å: Chain E: K.167, L.221, N.222, N.335, I.404, S.405 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.167, E:K.167 NAG-NAG-BMA-MAN.12: 6 residues within 4Å: Chain I: K.167, L.221, N.222, N.335, I.404, S.405 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:K.167, I:K.167

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

NAG.13: 4 residues within 4Å: Chain A: T.97, S.118, F.119, N.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.120 NAG.14: 3 residues within 4Å: Chain A: P.321, S.346, N.350 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.321 Hydrogen bonds: A:N.350 NAG.15: 3 residues within 4Å: Chain A: V.54, N.189, N.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.189, A:N.201 NAG.16: 2 residues within 4Å: Chain A: N.190, T.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.190 NAG.17: 4 residues within 4Å: Chain E: T.97, S.118, F.119, N.120 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.120 NAG.18: 3 residues within 4Å: Chain E: P.321, S.346, N.350 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:P.321 Hydrogen bonds: E:N.350 NAG.19: 3 residues within 4Å: Chain E: V.54, N.189, N.201 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.189, E:N.201 NAG.20: 2 residues within 4Å: Chain E: N.190, T.192 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.190 NAG.21: 4 residues within 4Å: Chain I: T.97, S.118, F.119, N.120 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.120 NAG.22: 3 residues within 4Å: Chain I: P.321, S.346, N.350 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:P.321 Hydrogen bonds: I:N.350 NAG.23: 3 residues within 4Å: Chain I: V.54, N.189, N.201 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.189, I:N.201 NAG.24: 2 residues within 4Å: Chain I: N.190, T.192 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.190

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 gp120: 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
M

B
B

F
F

J
N

C
C

G
G

K
O

D
D

H
H

L
P

Envelope glycoprotein gp120

Glycoprotein 41

CH235.12 Fab Heavy Chain

CH235.12 Fab Light Chain

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