SMTL ID : 8uls.1

Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 01_D03 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

24 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: E.55, N.56 Chain B: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.104, N.116, Y.133, D.288 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.133 NAG-NAG.3: 4 residues within 4Å: Chain A: T.96, Q.98, S.118, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain A: Q.261, N.263, N.299, S.301, R.410, V.412 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.269, I.290 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain A: N.263, T.265, H.297, N.299, T.381, R.410 Ligands: NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: S.355, N.359 Ligands: NAG-NAG-BMA-MAN.10, NAG-NAG-BMA-MAN.11, NAG-NAG-BMA-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.230, P.259, N.414 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: E.55, N.56 Chain D: G.13, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.104, N.116, Y.133, D.288 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.133 NAG-NAG.16: 5 residues within 4Å: Chain C: Q.98, S.118, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 7 residues within 4Å: Chain C: Q.261, N.263, N.299, S.301, R.410, V.412 Ligands: NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: N.269, I.290 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 7 residues within 4Å: Chain C: N.263, T.265, H.297, N.299, T.381, R.410 Ligands: NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain C: S.355, G.356, N.359 Ligands: NAG-NAG-BMA-MAN.24, NAG-NAG-BMA-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain E: E.55, N.56 Chain F: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain E: N.104, N.116, Y.133, D.288 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.133 NAG-NAG.29: 4 residues within 4Å: Chain E: T.96, Q.98, S.118, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 7 residues within 4Å: Chain E: Q.261, N.263, N.299, S.301, R.410, V.412 Ligands: NAG-NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain E: N.269, I.290 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 7 residues within 4Å: Chain E: N.263, T.265, H.297, N.299, T.381, R.410 Ligands: NAG-NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 5 residues within 4Å: Chain E: N.330, T.339, N.353 Ligands: NAG-NAG-BMA-MAN.37, NAG-NAG-BMA-MAN.37 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain E: S.355, G.356, N.359 Ligands: NAG-NAG-BMA-MAN.37, NAG-NAG-BMA-MAN.37 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain E: P.259, N.414 Ligands: NAG-NAG-BMA.31 No protein-ligand interaction detected (PLIP)

7 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.4: 5 residues within 4Å: Chain A: V.142, R.160, N.165, T.166 Chain C: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 10 residues within 4Å: Chain A: E.179, P.180, V.222, N.230, N.344, G.346, C.411, V.412, S.413 Ligands: NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain C: R.160, N.165, T.166 Chain E: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 9 residues within 4Å: Chain C: E.179, P.180, N.230, N.344, G.346, C.411, V.412, S.413 Ligands: NAG-NAG-BMA.26 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.412 NAG-NAG-BMA.26: 5 residues within 4Å: Chain C: L.233, P.259, V.412, N.414 Ligands: NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 5 residues within 4Å: Chain A: R.276 Chain E: V.142, R.160, N.165, T.166 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 10 residues within 4Å: Chain E: E.179, P.180, L.229, N.230, N.344, G.346, C.411, V.412, S.413 Ligands: NAG-NAG.39 No protein-ligand interaction detected (PLIP)

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.6: 14 residues within 4Å: Chain A: E.243, N.244 Chain H: Y.112, E.115, L.120, R.123 Chain K: T.30, N.31, A.32, H.49, D.50, S.52, T.53, Y.91 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.31, K:N.31, K:D.50, K:T.53 NAG-NAG-BMA-MAN-MAN.19: 14 residues within 4Å: Chain C: E.243, N.244 Chain I: Y.112, E.115, L.120, R.123 Chain L: T.30, N.31, A.32, H.49, D.50, S.52, T.53, Y.91 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:N.31, L:N.31, L:N.31, L:D.50, L:S.52, L:T.53 NAG-NAG-BMA-MAN-MAN.32: 14 residues within 4Å: Chain E: E.243, N.244 Chain G: Y.112, E.115, L.120, R.123 Chain J: T.30, N.31, A.32, H.49, D.50, T.53, F.67, Y.91 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.31, J:N.31, J:D.50, J:T.53

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 A: N.330, S.331, T.339, N.353 Ligands: NAG-NAG-BMA-MAN.11, NAG-NAG-BMA-MAN.11, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 6 residues within 4Å: Chain C: N.330, S.331, T.339, N.353 Ligands: NAG-NAG-BMA-MAN.24, NAG-NAG-BMA-MAN.24 No protein-ligand interaction detected (PLIP)

3 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.11: 6 residues within 4Å: Chain A: N.353, S.355 Ligands: NAG-NAG-BMA-MAN.10, NAG-NAG-BMA-MAN.10, NAG-NAG-BMA-MAN.10, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 6 residues within 4Å: Chain C: N.353, S.355 Ligands: NAG-NAG-BMA-MAN.23, NAG-NAG-BMA-MAN.23, NAG-NAG-BMA-MAN.23, NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.37: 5 residues within 4Å: Chain E: N.353, S.355 Ligands: NAG-NAG.36, NAG-NAG.36, NAG-NAG.38 No protein-ligand interaction detected (PLIP)

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

NAG.40: 2 residues within 4Å: Chain A: N.101, K.115 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: N.202, T.204, P.206 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: N.306, W.362 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain A: K.318, N.322 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain B: K.122, E.123, S.125, N.126, Y.127 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.101, K.115 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.202, T.204, P.206 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.306, W.362 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.322 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: E.123, N.126 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain E: N.101 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: N.202, T.204, P.206 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain E: N.306, W.362 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain E: N.322 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain F: E.123, N.126, Y.127 Ligand excluded by PLIP

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 01_D03 Fabs. To Be Published

Release Date

2025-04-16

Peptides

Envelope glycoprotein gp160: ACE
BG505 DS-SOSIP glycoprotein gp41: BDF
01_D03 Fab Heavy Chain: GHI
01_D03 Fab 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

01_D03 Fab Heavy Chain

01_D03 Fab Light Chain

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