SMTL ID : 8ulr.1

Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 05_B08 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

15 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.102, N.104, N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: Q.98, S.118, F.119, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain A: Q.261, N.263, N.299, V.300, S.301, S.379, R.410, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: N.263, T.265, H.297, N.299, T.381, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: N.353, S.355 Ligands: NAG-NAG-BMA-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: V.102, N.104, N.116, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: Q.98, S.118, F.119, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain C: Q.261, N.263, N.299, S.301, S.379, R.410, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: T.265, H.297, N.299, T.381 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain C: N.353, S.355 Ligands: NAG-NAG-BMA-MAN-MAN.17, NAG-NAG-BMA-MAN-MAN.17, NAG-NAG-BMA-MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain C: K.220, N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain E: Q.98, S.118, F.119, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 8 residues within 4Å: Chain E: Q.261, N.263, N.299, V.300, S.301, S.379, R.410, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain E: T.265, H.297, N.299, T.381 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain E: N.353, S.355 Ligands: NAG-NAG-BMA-MAN-MAN.27, NAG-NAG-BMA-MAN-MAN.27, NAG-NAG-BMA-MAN-MAN.27 No protein-ligand interaction detected (PLIP)

3 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.3: 5 residues within 4Å: Chain A: R.160, N.165, T.166 Chain C: R.276 Chain I: S.75 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 6 residues within 4Å: Chain C: R.160, N.165, T.166 Chain E: R.276 Chain H: R.19, S.75 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.19 NAG-NAG-BMA.20: 5 residues within 4Å: Chain E: V.102, N.104, N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP)

4 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.4: 6 residues within 4Å: Chain A: N.202, T.204, S.242, I.245, H.319 Chain L: F.67 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 7 residues within 4Å: Chain C: N.202, T.204, S.242, I.245, H.319 Chain K: Y.28, F.67 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.22: 5 residues within 4Å: Chain A: R.276 Chain E: R.160, N.165 Chain G: R.19, S.75 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.19 NAG-NAG-BMA-MAN.23: 7 residues within 4Å: Chain E: N.202, T.204, S.242, I.245, H.319 Chain J: Y.28, F.67 No protein-ligand interaction detected (PLIP)

2 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.5: 14 residues within 4Å: Chain A: S.177, E.179, P.180, L.229, N.230, R.272, N.344, C.345, G.346, Q.406, C.411, V.412, S.413 Ligands: NAG.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.412 NAG-NAG-BMA-MAN-MAN-MAN.14: 14 residues within 4Å: Chain C: S.177, E.179, P.180, L.229, N.230, R.272, N.344, C.345, G.346, Q.406, C.411, V.412, S.413 Ligands: NAG-NAG.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.412

3 x NAG- NAG- BMA- MAN- MAN: 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.8: 7 residues within 4Å: Chain A: N.330, S.331, T.339, N.353, S.355 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 7 residues within 4Å: Chain C: N.330, S.331, T.339, N.353, S.355 Ligands: NAG-NAG.18, NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.27: 7 residues within 4Å: Chain E: N.330, S.331, T.339, N.353, S.355 Ligands: NAG-NAG.28, NAG-NAG.28 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.24: 14 residues within 4Å: Chain E: K.175, S.177, E.179, P.180, L.229, N.230, R.272, N.344, C.345, G.346, C.411, V.412, S.413 Ligands: NAG.42 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:V.412, E:K.175, E:R.272, E:R.272

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

NAG.29: 4 residues within 4Å: Chain A: N.101, G.112, K.115, R.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.115, A:R.138 NAG.30: 8 residues within 4Å: Chain A: T.204, E.243, N.244 Chain L: Y.28, A.29, A.30, H.31, N.32 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain L Hydrogen bonds: A:N.244, L:Y.28, L:Y.28, L:N.32 NAG.31: 3 residues within 4Å: Chain A: N.269, I.290, V.408 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.408 Hydrogen bonds: A:N.269 NAG.32: 1 residues within 4Å: Chain A: N.322 No protein-ligand interaction detected (PLIP) NAG.33: 3 residues within 4Å: Chain A: V.412, N.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.412 NAG.34: 4 residues within 4Å: Chain C: N.101, G.112, K.115, R.138 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.115, C:R.138 NAG.35: 8 residues within 4Å: Chain C: T.204, E.243, N.244 Chain K: Y.28, A.29, A.30, H.31, N.32 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain C Hydrogen bonds: K:Y.28, K:Y.28, K:N.32, C:N.244 NAG.36: 3 residues within 4Å: Chain C: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG.37: 1 residues within 4Å: Chain C: N.322 No protein-ligand interaction detected (PLIP) NAG.38: 4 residues within 4Å: Chain E: N.101, G.112, K.115, R.138 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.115, E:R.138 NAG.39: 8 residues within 4Å: Chain E: T.204, E.243, N.244 Chain J: Y.28, A.29, A.30, H.31, N.32 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:Y.28, J:Y.28, J:N.32, E:N.244 NAG.40: 3 residues within 4Å: Chain E: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG.41: 1 residues within 4Å: Chain E: N.322 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.322 NAG.42: 3 residues within 4Å: Chain E: V.412, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.24 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeLaitsch, A.T. et al., Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 05_B08 Fabs. To Be Published

Release Date

2025-04-16

Peptides

Envelope glycoprotein gp160: ACE
BG505 DS-SOSIP glycoprotein gp41: BDF
05_B08 Fab Heavy Chain: GHI
05_B08 Light Chain: JKL

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

J
L

K
M

L
N

Envelope glycoprotein gp160

BG505 DS-SOSIP glycoprotein gp41

05_B08 Fab Heavy Chain

05_B08 Light Chain

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