SMTL ID : 9ogm.1

BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 and VRC01 Fabs (1x 10E8 Fab)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

hetero-3-3-1-3-1-3-3-mer

Ligands

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.1: 6 residues within 4Å: Chain N: N.248, I.249 Chain Q: Y.28, W.65, Y.89 Ligands: NAG.23 No protein-ligand interaction detected (PLIP)

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.2: 11 residues within 4Å: Chain N: S.181, E.183, P.184, V.226, L.233, N.234, N.348, G.350, V.416, S.417 Ligands: NAG.30 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:G.350, N:V.416

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN.3: 22 residues within 4Å: Chain A: D.27, S.28, R.29, H.33, R.98, R.102, I.103, Y.104, G.105, V.106, V.107, F.113 Chain B: S.50, S.51, Q.52 Chain N: N.267, T.269, D.296, R.298, H.301, N.303, S.383 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.9: 21 residues within 4Å: Chain C: D.27, S.28, R.29, H.33, R.98, R.102, I.103, Y.104, G.105, V.106, V.107, F.113 Chain D: S.50, S.51, Q.52 Chain O: N.267, T.269, D.296, R.298, N.303, T.385 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.107

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.4: 14 residues within 4Å: Chain A: S.34, D.51, H.53, N.55, A.57, T.58, T.59, W.112, H.114 Chain B: S.93, D.94, S.95 Chain N: S.359, N.363 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 5 residues within 4Å: Chain O: T.107, N.120, Y.137, L.139, D.292 1 PLIP interactions: 1 interactions with chain O Hydrophobic interactions: O:Y.137 NAG-NAG.6: 4 residues within 4Å: Chain L: Y.75 Chain N: R.280 Chain O: R.164, N.169 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain O: Q.334, T.343, N.357, S.359 Ligands: NAG-NAG-BMA-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain G: R.53 Chain P: V.106, N.120, Y.137, D.292 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:Y.137 NAG-NAG.16: 3 residues within 4Å: Chain P: N.357, S.359 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.17 No protein-ligand interaction detected (PLIP)

2 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.7: 11 residues within 4Å: Chain O: E.36, S.181, P.184, L.233, N.234, N.348, G.350, C.415, V.416, S.417 Ligands: NAG.39 2 PLIP interactions: 2 interactions with chain O Hydrophobic interactions: O:V.416 Hydrogen bonds: O:G.350 NAG-NAG-BMA-MAN-MAN.14: 7 residues within 4Å: Chain J: Y.28, G.29, W.65, G.66, Y.89 Chain P: N.248 Ligands: NAG.44 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-[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.8: 12 residues within 4Å: Chain M: Y.28, G.29, S.30, S.63, R.64, W.65, G.66, D.68, Y.69, Y.89 Chain O: N.248 Ligands: NAG.35 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:G.29

2 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 C: N.55, A.57 Chain O: S.359, G.360, N.363 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.55 NAG-NAG-BMA-MAN.13: 7 residues within 4Å: Chain P: L.233, N.234, N.348, C.349, V.416, S.417 Ligands: NAG.47 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:V.416 Hydrogen bonds: P:V.416

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN.15: 21 residues within 4Å: Chain F: D.27, S.28, R.29, H.33, R.98, R.102, I.103, Y.104, G.105, V.106, V.107, F.113 Chain G: S.50, S.51, Q.52 Chain P: N.267, T.269, D.296, H.301, N.303, R.414 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:V.107 Hydrogen bonds: F:V.107

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.17: 15 residues within 4Å: Chain F: D.51, N.55, A.57, T.58, T.59, W.112, H.114 Chain G: S.93, D.94, S.95, K.97 Chain P: S.359, N.363 Ligands: NAG-NAG.16, NAG-NAG.16 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:T.59, F:H.114, G:K.97

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

NAG.18: 2 residues within 4Å: Chain A: V.2, N.26 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.26 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain F: N.26 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: G.56, A.63 Chain N: N.109, I.110 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain N: T.100, Q.102, S.122, F.123, N.124, K.135 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain N: K.204, N.206, T.208, P.210 Ligands: NAG-NAG-BMA.1 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain N: N.273, I.294, V.412 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain N: N.105 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain N: V.106, N.120, L.139 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain K: D.73, Y.75 Chain N: V.146, R.164, N.169, T.170 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain N: K.306, N.310, W.366 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain N: T.344, N.357, S.359, R.389 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain N: P.263, V.416, N.418 Ligands: NAG-NAG-BMA-MAN.2 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain N: Q.265, N.267, N.303, S.305, R.414 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain O: N.105, M.114 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: S.55 Chain O: N.109 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain O: Q.102, S.122, N.124, K.135 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain O: N.206, T.208, S.246 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.8 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain O: Q.265, N.267, S.305, R.414 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain O: N.273, I.294 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain O: N.310, W.366 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain O: N.234, P.263, N.418 Ligands: NAG-NAG-BMA-MAN-MAN.7 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain P: N.105 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: S.54 Chain P: N.109 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain P: Q.102, S.122, F.123, N.124, K.135 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain H: Y.75 Chain O: R.280 Chain P: R.164, N.169, T.170 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain P: N.206, T.208, I.249 Ligands: NAG-NAG-BMA-MAN-MAN.14 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain P: Q.265, N.267, V.304, S.305, S.383, R.414 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain P: N.273, I.294, V.412 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain P: N.234, P.263, N.418 Ligands: NAG-NAG-BMA-MAN.13 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rantalainen, K. et al., Virus glycoprotein nanodisc platform for vaccine design. Biorxiv (2025)

Release Date

2025-07-30

Peptides

BG18 Fab heavy chain: ACF
BG18 Fab light chain: BDG
10E8 Fab heavy chain: E
VRC01 Fab heavy chain: HKL
10E8 Fab light chain: I
VRC01 Fab light chain: JMQ
Envelope glycoprotein gp160: NOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
F

F
I

B
E

D
G

G
J

E
H

H
K

K
N

L
P

I
L

J
M

M
Q

Q
O

N
A

O
B

P
C

BG18 Fab heavy chain

BG18 Fab light chain

10E8 Fab heavy chain

VRC01 Fab heavy chain

10E8 Fab light chain

VRC01 Fab light chain

Envelope glycoprotein gp160

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