SMTL ID : 8tng.1

Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody R27 targeting the CD4-binding site

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

19 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: 3 residues within 4Å: Chain A: N.106, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.246 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.265, N.301, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: E.57, N.58 Chain D: G.16 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: V.104, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: Q.100, S.120, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.265, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: T.267, H.299, N.301, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: N.332, S.333, T.341, N.355 Ligands: NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: V.104, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain E: N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain E: N.265, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: H.299, N.301, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain E: N.332, S.333, T.341, N.355 Ligands: NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.21, NAG.46 No protein-ligand interaction detected (PLIP)

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.2: 6 residues within 4Å: Chain A: E.181, N.232, N.346, V.414, S.415 Ligands: NAG.29 No protein-ligand interaction detected (PLIP)

2 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.10: 6 residues within 4Å: Chain C: K.35, E.181, L.231, N.232, V.414 Ligands: NAG.37 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.35, C:K.35 NAG-NAG-BMA-MAN.17: 8 residues within 4Å: Chain E: K.35, E.181, L.231, N.232, N.346, V.414, S.415 Ligands: NAG.47 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.181, E:K.35

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

NAG.23: 4 residues within 4Å: Chain A: E.57, N.58 Chain B: F.8, S.17 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: T.98, Q.100, N.122 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.204, S.244 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: C.266, T.267, H.299, N.301, S.381 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.361 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: P.261, N.416 Ligands: NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.308 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.271 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: R.162, N.167, T.168 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.126, Y.127 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.103, G.114, K.117, R.140 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.361 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.10 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: R.162, N.167, T.168 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.271, I.292 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: E.57, N.58 Chain F: S.17 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: Q.100, N.122 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: N.204, T.206, S.244 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain E: N.271 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.22, NAG-NAG.22 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: P.261, N.416 Ligands: NAG-NAG-BMA-MAN.17 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: R.162, N.167, T.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, J. et al., Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody R27 targeting the CD4-binding site. To Be Published

Release Date

2024-05-08

Peptides

HIV-1 BG505 DS-SOSIP gp120: ACE
Envelope glycoproteiHIV-1 BG505 DS-SOSIP gp41n gp41: BDF
CD4-binding site targeting nanobody R27: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

H
I

I
J

HIV-1 BG505 DS-SOSIP gp120

Envelope glycoproteiHIV-1 BG505 DS-SOSIP gp41n gp41

CD4-binding site targeting nanobody R27

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