SMTL ID : 8dow.1

Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

9 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: 2 residues within 4Å: Chain A: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: K.320, N.322, R.427 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.263, T.265, I.284 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain E: N.400, I.401, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain E: K.320, N.322, R.427 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain E: N.263, I.284 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain I: N.400, I.401, T.402 Chain L: D.33 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:D.33 NAG-NAG.13: 1 residues within 4Å: Chain I: N.352 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain I: N.322, R.427 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.2: 18 residues within 4Å: Chain A: T.259, H.291, N.293, T.371, T.373 Chain C: R.98, P.101, Y.103, R.104, Y.105, W.106, H.111, D.113 Chain D: R.51, Y.54, E.55, D.60, S.61 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.105 Hydrogen bonds: C:R.104, C:Y.105 NAG-NAG-BMA-MAN-MAN-MAN.7: 18 residues within 4Å: Chain E: T.259, H.291, N.293, T.371, T.373 Chain G: R.98, Y.103, R.104, Y.105, W.106, G.109, H.111, D.113 Chain H: R.51, Y.54, E.55, D.60, S.61 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.105 Hydrogen bonds: G:R.104, G:Y.105, G:Y.103 NAG-NAG-BMA-MAN-MAN-MAN.11: 18 residues within 4Å: Chain I: T.259, H.291, N.293, T.371, T.373 Chain K: R.98, Y.103, R.104, Y.105, W.106, G.109, H.111, D.113 Chain L: R.51, Y.54, E.55, D.60, S.61 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:Y.105 Hydrogen bonds: K:Y.105, K:Y.103

3 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.3: 7 residues within 4Å: Chain A: T.171, L.223, N.224, C.403, R.404, S.405 Ligands: NAG.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.404, A:T.171, A:T.171 NAG-NAG-BMA-MAN.10: 6 residues within 4Å: Chain E: E.173, L.223, N.224, R.404, S.405 Ligands: NAG.26 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.404, E:T.171 NAG-NAG-BMA-MAN.15: 5 residues within 4Å: Chain I: E.173, N.224, R.404, S.405 Ligands: NAG.31 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:R.404

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.16: 2 residues within 4Å: Chain I: N.263, I.284 No protein-ligand interaction detected (PLIP)

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

NAG.17: 4 residues within 4Å: Chain A: A.104, N.116, Y.133, D.282 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: T.332, N.346, S.348 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: V.142, R.154, N.159 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.316 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.224, P.253, N.406 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: W.66, N.196, T.198, S.236, E.237 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain E: T.332, N.346, S.348 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain E: R.154, N.159 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain E: N.316 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain E: N.224, P.253, N.406 Ligands: NAG-NAG-BMA-MAN.10 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain E: A.104, N.116, Y.133, D.282 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain E: W.66, N.196, T.198, S.236, E.237 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain I: N.316 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain I: A.104, N.116, Y.133, D.282 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain I: P.253, N.406 Ligands: NAG-NAG-BMA-MAN.15 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain I: T.332, N.346, S.348 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain I: V.142, R.154, N.159 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain I: W.66, N.196, T.198, S.236 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Shared recognition mechanism for HIV-1 envelope-reactive V3 glycan broadly neutralizing B cell lineage maturation in humans and macaques. To Be Published

Release Date

2023-07-19

Peptides

Envelope glycoprotein gp120: AEI
Envelope glycoprotein gp41: BFJ
DH1030.1 Fab Heavy chain: CGK
DH1030.1 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 gp120

Envelope glycoprotein gp41

DH1030.1 Fab Heavy chain

DH1030.1 Fab Light Chain

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