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SMTL ID : 8tnh.1

Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody G36 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:	5 residues within 4Å: Chain A: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP)
NAG-NAG.3:	2 residues within 4Å: Chain A: N.246, N.249 No protein-ligand interaction detected (PLIP)
NAG-NAG.4:	3 residues within 4Å: Chain A: N.265, V.302, S.303 No protein-ligand interaction detected (PLIP)
NAG-NAG.5:	7 residues within 4Å: Chain A: N.332, S.333, S.334, T.341, S.357 Ligands: NAG-NAG.6, 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:	4 residues within 4Å: Chain C: E.57, N.58 Chain D: F.8, S.17 No protein-ligand interaction detected (PLIP)
NAG-NAG.8:	4 residues within 4Å: Chain C: V.104, N.106, N.118, Y.135 No protein-ligand interaction detected (PLIP)
NAG-NAG.9:	2 residues within 4Å: Chain C: 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:	4 residues within 4Å: Chain C: Q.263, N.265, S.303, V.414 No protein-ligand interaction detected (PLIP)
NAG-NAG.13:	5 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, S.381 No protein-ligand interaction detected (PLIP)
NAG-NAG.14:	6 residues within 4Å: Chain C: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.15, NAG-NAG.15 No protein-ligand interaction detected (PLIP)
NAG-NAG.15:	5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.14, NAG-NAG.14, NAG.36 No protein-ligand interaction detected (PLIP)
NAG-NAG.16:	5 residues within 4Å: Chain E: V.104, N.118, Y.135, L.137, D.290 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:	2 residues within 4Å: Chain E: N.265, S.303 No protein-ligand interaction detected (PLIP)
NAG-NAG.20:	4 residues within 4Å: Chain E: T.267, H.299, N.301, S.381 No protein-ligand interaction detected (PLIP)
NAG-NAG.21:	6 residues within 4Å: Chain E: N.332, S.333, T.341, N.355, S.357 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, L.231, N.232, 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:	7 residues within 4Å: Chain C: K.35, E.181, N.232, N.346, V.414, S.415 Ligands: NAG.37 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.35, C:K.35
NAG-NAG-BMA-MAN.17:	7 residues within 4Å: Chain E: K.35, E.181, L.231, N.232, V.414, S.415 Ligands: NAG.47 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.35, E:K.35

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

NAG.23:	2 residues within 4Å: Chain A: N.58 Chain B: S.17 Ligand excluded by PLIP
NAG.24:	2 residues within 4Å: Chain A: N.103, K.117 Ligand excluded by PLIP
NAG.25:	3 residues within 4Å: Chain A: Q.100, N.122, K.133 Ligand excluded by PLIP
NAG.26:	2 residues within 4Å: Chain A: N.204, T.206 Ligand excluded by PLIP
NAG.27:	4 residues within 4Å: Chain A: T.267, H.299, N.301, S.381 Ligand excluded by PLIP
NAG.28:	2 residues within 4Å: Chain A: R.329, 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:	3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP
NAG.32:	3 residues within 4Å: Chain A: R.162, N.167 Chain E: E.126 Ligand excluded by PLIP
NAG.33:	1 residues within 4Å: Chain B: N.126 Ligand excluded by PLIP
NAG.34:	2 residues within 4Å: Chain C: N.103, K.117 Ligand excluded by PLIP
NAG.35:	3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP
NAG.36:	2 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG.15 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:	2 residues within 4Å: Chain C: N.271, V.410 Ligand excluded by PLIP
NAG.40:	2 residues within 4Å: Chain A: R.278 Chain C: N.167 Ligand excluded by PLIP
NAG.41:	2 residues within 4Å: Chain E: N.58 Chain F: S.17 Ligand excluded by PLIP
NAG.42:	2 residues within 4Å: Chain E: N.103, K.117 Ligand excluded by PLIP
NAG.43:	2 residues within 4Å: Chain E: N.122, K.133 Ligand excluded by PLIP
NAG.44:	3 residues within 4Å: Chain E: N.204, T.206, P.208 Ligand excluded by PLIP
NAG.45:	2 residues within 4Å: Chain E: N.271, I.292 Ligand excluded by PLIP
NAG.46:	2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.22 Ligand excluded by PLIP
NAG.47:	2 residues within 4Å: Chain E: 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:	4 residues within 4Å: Chain C: E.126 Chain E: I.146, R.162, N.167 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 G36 targeting the CD4-binding site. To Be Published

Release Date

2024-05-08

Peptides

HIV-1 BG505 DS-SOSIP gp120: ACE
HIV-1 BG505 DS-SOSIP gp41: BDF
CD4-binding site nanobody G36: 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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

HIV-1 BG505 DS-SOSIP gp120

Toggle Identical (ACE)

HIV-1 BG505 DS-SOSIP gp41

Toggle Identical (DF)

CD4-binding site nanobody G36

Toggle Identical (GHI)

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