SMTL ID : 9ber.1

Cryo-EM structure of the HIV-1 JR-FL IDL Env trimer in complex with PGT122 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

12 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: 4 residues within 4Å: Chain A: N.124, K.139, Y.141, G.287 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: V.55, N.197, N.209 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: M.339, N.352, T.354 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.230, N.412 Ligands: NAG-NAG-BMA-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.124, K.139, Y.141, G.287 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.141 NAG-NAG.8: 5 residues within 4Å: Chain C: E.53, V.55, N.197, K.208, N.209 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.53 NAG-NAG.10: 3 residues within 4Å: Chain C: M.339, N.352, T.354 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.230, N.412 Ligands: NAG-NAG-BMA-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: N.124, Y.141 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.141 NAG-NAG.14: 2 residues within 4Å: Chain E: N.197, N.209 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: M.339, N.352, T.354 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain E: N.230, S.259, N.412 Ligands: NAG-NAG-BMA-MAN.15 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.3: 8 residues within 4Å: Chain A: E.179, P.180, V.222, N.230, N.343, S.410, S.411 Ligands: NAG-NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.410, A:E.179 NAG-NAG-BMA-MAN.9: 10 residues within 4Å: Chain C: E.179, P.180, L.229, N.230, F.342, N.343, R.408, S.410, S.411 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.179 NAG-NAG-BMA-MAN.15: 9 residues within 4Å: Chain E: D.32, E.179, P.180, L.229, N.230, N.343, S.410, S.411 Ligands: NAG-NAG.17 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.410

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.6: 11 residues within 4Å: Chain A: R.294, H.297, N.299, N.374, T.375 Chain G: R.103, I.104, Y.105, G.106 Chain H: N.42, P.58 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:G.106, A:R.294 NAG-NAG-BMA-MAN-MAN-MAN.12: 12 residues within 4Å: Chain C: H.297, N.299, N.374, T.375, T.377 Chain I: R.103, I.104, G.106, V.107 Chain J: N.42, N.44, P.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.18: 13 residues within 4Å: Chain E: T.265, R.294, H.297, N.299, T.375, T.377 Chain K: R.103, I.104, G.106, V.107 Chain L: N.44, P.58, S.60 No protein-ligand interaction detected (PLIP)

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

NAG.19: 3 residues within 4Å: Chain A: E.57, N.58 Chain B: T.18 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.128 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: D.243, N.244, T.246 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.261, N.263 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.269, Q.406 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: A.303, N.306, W.361 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: F.327, N.328, I.431 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Q.355, N.358 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: V.150, R.160, N.165 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.202, T.204 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.322 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.155 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: R.110, N.114 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.126 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.58 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.128, V.137 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.244, T.246 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.261, N.263 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.269, I.290, Q.406 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: A.303, N.306, W.361 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.328, H.329 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.358 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: I.152, I.162, N.165 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: T.200, N.202, T.204 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: R.317, N.322 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.155 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain D: N.126 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain D: N.114 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain D: N.105 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: E.57, N.58 Chain F: N.114 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain E: N.100, N.128, K.139 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: N.244, T.246, N.247 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: N.263, R.408 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain E: N.269, I.290 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain E: A.303, N.306, W.361 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain E: N.328, I.431 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain E: N.358 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain E: I.152, N.165 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain E: N.202, T.204 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain E: N.155 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain F: R.122, N.126 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, P. et al., Design of soluble HIV-1 envelope trimers free of covalent gp120-gp41 bonds with prevalent native-like conformation. Cell Rep (2024)

Release Date

2024-07-31

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
PGT122 heavy chain: GIK
PGT122 light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
A

E
F

B
B

D
C

F
I

G
H

I
D

K
J

H
L

J
E

L
K

Envelope glycoprotein gp120

Envelope glycoprotein gp41

PGT122 heavy chain

PGT122 light chain

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