SMTL ID : 9bf6.1

Cryo-EM structure of the HIV-1 WITO 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- 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 B: E.53, V.55, N.199, N.211 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.53, B:V.55 NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: A.18, N.19, N.69, E.72 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain B: H.100, S.126, N.128, K.139 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain B: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain F: E.53, N.199, N.211 Ligands: NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain F: A.18, N.19, N.69, E.72 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain F: H.100, N.128, K.139 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain F: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain J: E.53, V.55, N.199, N.211 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:E.53, J:V.55 NAG-NAG-BMA.17: 3 residues within 4Å: Chain J: N.19, N.69, E.72 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain J: H.100, N.128, K.139 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain J: R.162, N.167 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.2: 13 residues within 4Å: Chain B: S.179, E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, Q.409, S.413, S.414 Ligands: NAG.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.181, B:G.348, B:S.413 NAG-NAG-BMA-MAN-MAN-MAN.4: 10 residues within 4Å: Chain B: T.267, H.299, N.301, N.378, T.380 Chain C: R.103, I.104, G.106, V.108 Chain D: S.60 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.104, C:V.108 Hydrophobic interactions: C:V.108 NAG-NAG-BMA-MAN-MAN-MAN.9: 13 residues within 4Å: Chain F: S.179, E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, G.408, S.413, S.414 Ligands: NAG.47 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.181, F:G.348, F:S.413 NAG-NAG-BMA-MAN-MAN-MAN.11: 11 residues within 4Å: Chain F: T.267, H.299, N.301, N.378, T.380 Chain G: R.103, I.104, G.106, V.108 Chain H: N.43, S.60 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:I.104, G:V.108 Hydrophobic interactions: G:V.108 NAG-NAG-BMA-MAN-MAN-MAN.16: 12 residues within 4Å: Chain J: S.179, E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, S.413, S.414 Ligands: NAG.63 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:E.181, J:G.348, J:S.413 NAG-NAG-BMA-MAN-MAN-MAN.18: 10 residues within 4Å: Chain J: T.267, H.299, N.301, N.378, T.380 Chain K: R.103, I.104, G.106, V.108 Chain L: S.60 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:I.104, K:V.108 Hydrophobic interactions: K:V.108

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.6: 6 residues within 4Å: Chain B: V.104, M.118, N.124, Y.141, G.289, A.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 4 residues within 4Å: Chain F: M.118, N.124, Y.141, G.289 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.20: 3 residues within 4Å: Chain J: M.118, N.124, Y.141 No protein-ligand interaction detected (PLIP)

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

NAG.22: 3 residues within 4Å: Chain A: R.122, N.126, Y.127 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.100, T.101 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.113, N.114 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.105 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.58 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.246, T.248 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: K.263, N.265, S.303, N.378 Ligands: NAG.34 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.271, I.292, Q.409 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: I.329, N.331, R.436 Ligands: NAG.35 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.355, T.357 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain B: N.232, L.235, P.261, N.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.2 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.103 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.378 Ligands: NAG.28 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain B: N.331, Q.332, T.357, N.361 Ligands: NAG.30 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: N.200, T.202, F.203, R.210, N.211 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: R.122, N.126, Y.127 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain E: N.100, T.101 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain E: N.113, N.114 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain E: N.105 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain F: N.58 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain F: N.246, T.248 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain F: K.263, N.265, S.303, N.378 Ligands: NAG.49 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain F: N.271, I.292, Q.409 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain F: I.329, N.331, R.436 Ligands: NAG.50 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain F: M.342, N.355, T.357 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain F: N.232, L.235, P.261, N.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.9 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain F: N.103 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain F: N.378 Ligands: NAG.43 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain F: N.331, Q.332, T.357, N.361 Ligands: NAG.45 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain F: N.200, T.202, R.210, N.211 Ligands: NAG-NAG-BMA.8 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain I: N.126, Y.127 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain I: N.100, T.101 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain I: N.113, N.114 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain I: N.105 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain J: G.57, N.58 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain J: N.246, T.248 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain J: K.263, N.265, S.303, N.378 Ligands: NAG.65 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain J: N.271, I.292, Q.409 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain J: I.329, N.331, R.436 Ligands: NAG.66 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain J: M.342, N.355, T.357, R.384 Ligand excluded by PLIP NAG.63: 5 residues within 4Å: Chain J: N.232, L.235, P.261, N.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain J: N.103 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain J: N.378 Ligands: NAG.59 Ligand excluded by PLIP NAG.66: 5 residues within 4Å: Chain J: N.331, Q.332, T.357, N.361 Ligands: NAG.61 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain J: N.200, T.202, F.203, R.210 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.52: 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 gp41: AEI
Envelope glycoprotein gp120: BFJ
PGT122 heavy chain: CGK
PGT122 light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
B

I
I

B
C

F
F

J
J

C
D

G
G

K
K

D
E

H
H

L
L

Envelope glycoprotein gp41

Envelope glycoprotein gp120

PGT122 heavy chain

PGT122 light chain

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