SMTL ID : 7t9t.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-NAG.1: 8 residues within 4Å: Chain C: R.3 Chain I: D.171, P.172, N.222, N.335, C.336, C.403, I.404 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.3, C:R.3 NAG-NAG-BMA-NAG.7: 7 residues within 4Å: Chain A: D.171, P.172, N.222, N.335, C.336, I.404 Chain G: R.3 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.3, G:R.3 NAG-NAG-BMA-NAG.13: 8 residues within 4Å: Chain E: D.171, P.172, N.222, N.335, C.336, C.403, I.404 Chain K: R.3 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.3, K:R.3

6 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: 3 residues within 4Å: Chain I: S.118, F.119, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: E.294, N.298, R.351, R.370 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: S.118, F.119, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: E.294, S.295, N.298, R.351 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain E: S.118, F.119, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain I: E.294, S.295, N.298, R.351 No protein-ligand interaction detected (PLIP)

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.3: 2 residues within 4Å: Chain I: N.350 Ligands: NAG-NAG-BMA.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain A: T.331, N.344, S.346, R.377 Ligands: NAG-NAG-BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 3 residues within 4Å: Chain A: S.346, N.350 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 5 residues within 4Å: Chain E: T.331, N.344, S.346, R.377 Ligands: NAG-NAG-BMA.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 2 residues within 4Å: Chain E: N.350 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 5 residues within 4Å: Chain I: T.331, N.344, S.346, R.377 Ligands: NAG-NAG-BMA.3 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.4: 10 residues within 4Å: Chain I: R.152, N.157, T.158 Chain K: S.69, Y.71, D.73, S.75, Y.80, D.82, R.84 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.71 NAG-NAG-BMA-MAN-MAN-MAN.10: 10 residues within 4Å: Chain A: R.152, N.157, T.158 Chain C: S.69, Y.71, D.73, S.75, M.76, Y.80, D.82 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.71 NAG-NAG-BMA-MAN-MAN-MAN.16: 10 residues within 4Å: Chain E: R.152, N.157, T.158 Chain G: S.69, Y.71, D.73, S.75, M.76, Y.80, D.82 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.71

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

NAG.19: 2 residues within 4Å: Chain A: N.190, N.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.190, A:N.200 NAG.20: 6 residues within 4Å: Chain A: E.52, V.54, N.189, N.201, V.202, S.203 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.189 Hydrogen bonds: A:N.189 NAG.21: 2 residues within 4Å: Chain E: N.190, N.200 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.190, E:N.200 NAG.22: 6 residues within 4Å: Chain E: E.52, V.54, N.189, N.201, V.202, S.203 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:N.189 Hydrogen bonds: E:N.189 NAG.23: 3 residues within 4Å: Chain I: N.190, T.192, N.200 No protein-ligand interaction detected (PLIP) NAG.24: 6 residues within 4Å: Chain I: E.52, V.54, N.189, N.201, V.202, S.203 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:N.189 Hydrogen bonds: I:N.189

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

2023-08-16

Peptides

Envelope glycoprotein gp160: AEI
Envelope glycoprotein gp41: 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

Envelope glycoprotein gp41

CH235.12 Fab Heavy Chain

CH235.12 Fab Light Chain

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