SMTL ID : 8ulu.1

Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 and PGDM1400 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-3-1-3-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.4: 3 residues within 4Å: Chain A: V.142, R.160, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.202, T.204, S.242, H.319 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: N.244 Chain L: D.28, V.29, G.30, W.31 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: N.263, N.299, V.300, S.301, S.379, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: N.269, I.290 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: T.265, H.297, N.299, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain A: N.330, T.339, N.353, S.355 Ligands: NAG-NAG.12, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: N.353, S.355 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: V.102, N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.202 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain C: E.243, N.244 Chain J: D.115 Chain N: V.29, W.31, T.50 Ligands: NAG-NAG.15 1 PLIP interactions: 1 interactions with chain N Hydrophobic interactions: N:T.50 NAG-NAG.17: 4 residues within 4Å: Chain C: N.263, N.299, S.301, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: N.269, I.290 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain C: N.263, T.265, H.297, N.299, T.381, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain C: N.353, S.355 Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain E: N.202, T.204 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 7 residues within 4Å: Chain E: N.244 Chain I: D.115 Chain M: D.28, V.29, G.30, W.31, T.50 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:W.31, M:T.50 Hydrogen bonds: M:W.31 NAG-NAG.30: 6 residues within 4Å: Chain E: Q.261, N.263, V.300, S.301, R.410, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain E: N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain E: T.265, H.297, N.299, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain E: N.330, S.331, T.339 Ligands: NAG-NAG.34, NAG-NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 4 residues within 4Å: Chain E: N.353, S.355 Ligands: NAG-NAG.33, NAG-NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain E: P.259, Q.261, N.414 Ligands: NAG-NAG-BMA-MAN.28 No protein-ligand interaction detected (PLIP)

5 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: 4 residues within 4Å: Chain A: V.102, N.116, Y.133, L.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain C: N.330, N.353 Ligands: NAG-NAG.21, NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 6 residues within 4Å: Chain C: R.160, N.165 Chain E: R.276 Chain J: R.19, D.84, S.86 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:R.19 NAG-NAG-BMA.24: 4 residues within 4Å: Chain E: V.102, N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 5 residues within 4Å: Chain E: V.142, R.160, N.165 Chain I: R.19, S.86 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.19

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.3: 7 residues within 4Å: Chain A: T.96, S.118, F.119, N.120 Chain K: G.55, D.56, K.58 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.56 NAG-NAG-BMA-MAN-MAN.6: 11 residues within 4Å: Chain A: K.33, P.180, V.222, L.229, N.230, N.344, G.346, C.411, V.412, S.413 Ligands: NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 7 residues within 4Å: Chain C: E.179, L.229, N.230, N.344, V.412, S.413 Ligands: NAG.40 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.14: 15 residues within 4Å: Chain C: T.96, Q.98, S.118, F.119, N.120 Chain G: H.31, G.32, R.97, S.99 Chain K: D.106, Y.107, W.118, V.120, V.122, Y.124 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain C Hydrophobic interactions: K:V.120 Hydrogen bonds: C:Q.98

1 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.25: 15 residues within 4Å: Chain A: D.127 Chain E: T.96, Q.98, N.120 Chain G: N.35, Y.37 Chain K: T.31, Y.32, H.53, S.100, K.101, H.102, R.103, L.104, Y.110 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain G Hydrophobic interactions: K:L.104 Hydrogen bonds: K:R.103, K:R.103, G:N.35, G:Y.37, G:Y.37

1 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.28: 9 residues within 4Å: Chain E: E.179, P.180, K.220, L.229, N.230, G.346, V.412, S.413 Ligands: NAG-NAG.35 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.179, E:E.179

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

NAG.36: 1 residues within 4Å: Chain A: N.306 No protein-ligand interaction detected (PLIP) NAG.37: 3 residues within 4Å: Chain A: P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG.38: 3 residues within 4Å: Chain C: E.55, N.56 Chain D: S.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.55 NAG.39: 3 residues within 4Å: Chain C: K.302, N.306, W.362 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.302 NAG.40: 3 residues within 4Å: Chain C: P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.22 No protein-ligand interaction detected (PLIP) NAG.41: 3 residues within 4Å: Chain E: E.55, N.56 Chain F: S.17 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.55 Hydrogen bonds: E:N.56 NAG.42: 2 residues within 4Å: Chain E: N.306, W.362 No protein-ligand interaction detected (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 04_A06 PGDM1400 Fabs. To Be Published

Release Date

2025-04-16

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
PGDM1400 Fab Light Chain: G
04_A06 Fab Heavy Chain: HIJ
PGDM1400 Fab Heavy Chain: K
04_A06 Fab Light Chain: LMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Envelope glycoprotein gp120

Envelope glycoprotein gp41

PGDM1400 Fab Light Chain

04_A06 Fab Heavy Chain

PGDM1400 Fab Heavy Chain

04_A06 Fab Light Chain

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