SMTL ID : 6cde.1

Cryo-EM structure at 3.8 A resolution of vaccine-elicited antibody vFP20.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

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

Ligands

18 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: 2 residues within 4Å: Chain G: K.122, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 1 residues within 4Å: Chain G: N.100 2 PLIP interactions: 2 interactions with chain W Hydrogen bonds: W:Y.32, W:Y.32 NAG-NAG-BMA.12: 3 residues within 4Å: Chain H: N.271, T.273, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 7 residues within 4Å: Chain H: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN.15, NAG-NAG-BMA-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 3 residues within 4Å: Chain H: N.361 Ligands: NAG-NAG-BMA-MAN.15, NAG-NAG-BMA-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 5 residues within 4Å: Chain H: P.261, N.416 Chain J: K.24, D.75 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.10 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:K.24, J:K.24, J:K.24 NAG-NAG-BMA.18: 2 residues within 4Å: Chain O: K.122, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 1 residues within 4Å: Chain O: N.100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 3 residues within 4Å: Chain P: N.271, T.273, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 7 residues within 4Å: Chain P: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN.32, NAG-NAG-BMA-MAN.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 3 residues within 4Å: Chain P: N.361 Ligands: NAG-NAG-BMA-MAN.32, NAG-NAG-BMA-MAN.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 5 residues within 4Å: Chain B: K.24, D.75 Chain P: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.24, B:K.24, B:K.24 NAG-NAG-BMA.35: 2 residues within 4Å: Chain U: K.122, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 1 residues within 4Å: Chain U: N.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32 NAG-NAG-BMA.46: 3 residues within 4Å: Chain V: N.271, T.273, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.48: 7 residues within 4Å: Chain V: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN.49, NAG-NAG-BMA-MAN.49 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.50: 3 residues within 4Å: Chain V: N.361 Ligands: NAG-NAG-BMA-MAN.49, NAG-NAG-BMA-MAN.49 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.51: 5 residues within 4Å: Chain V: P.261, N.416 Chain X: K.24, D.75 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.44 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:K.24, X:K.24, X:K.24

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

NAG-NAG.3: 2 residues within 4Å: Chain H: N.58 Chain I: Y.57 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain H: T.102, N.103, I.108, D.110 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain H: R.162, I.164, N.167 Chain V: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain H: N.265, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain A: Y.57 Chain P: N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain P: T.102, N.103, I.108, D.110 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain H: R.278 Chain P: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain P: N.265, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 2 residues within 4Å: Chain V: N.58 Chain W: Y.57 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain V: T.102, N.103, I.108, D.110 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 4 residues within 4Å: Chain P: R.278 Chain V: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 4 residues within 4Å: Chain V: N.265, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP)

3 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.5: 8 residues within 4Å: Chain C: D.56, N.58, F.114, T.115 Chain D: W.88, D.89, T.94 Chain H: N.107 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.56, C:N.58, C:T.115 NAG-NAG-BMA-MAN.22: 8 residues within 4Å: Chain K: D.56, N.58, F.114, T.115 Chain L: W.88, D.89, T.94 Chain P: N.107 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:D.56, K:N.58, K:T.115 NAG-NAG-BMA-MAN.39: 8 residues within 4Å: Chain Q: D.56, N.58, F.114, T.115 Chain R: W.88, D.89, T.94 Chain V: N.107 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:D.56, Q:N.58, Q:T.115

3 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.6: 8 residues within 4Å: Chain D: E.20 Chain H: V.104, T.105, N.118, S.120, Y.135, D.290 Ligands: MAN.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.23: 8 residues within 4Å: Chain L: E.20 Chain P: V.104, T.105, N.118, S.120, Y.135, D.290 Ligands: MAN.57 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.40: 8 residues within 4Å: Chain R: E.20 Chain V: V.104, T.105, N.118, S.120, Y.135, D.290 Ligands: MAN.61 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.7: 5 residues within 4Å: Chain H: Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.24: 5 residues within 4Å: Chain P: Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.41: 5 residues within 4Å: Chain V: Q.100, S.120, N.122, K.131, K.133 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.9: 6 residues within 4Å: Chain H: N.204, T.206, S.244, E.245, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.26: 6 residues within 4Å: Chain P: N.204, T.206, S.244, E.245, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.43: 6 residues within 4Å: Chain V: N.204, T.206, S.244, E.245, I.247, H.321 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.10: 8 residues within 4Å: Chain H: S.179, E.181, N.232, N.346, V.414, S.415 Chain N: Q.1 Ligands: NAG-NAG-BMA.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27: 8 residues within 4Å: Chain P: S.179, E.181, N.232, N.346, V.414, S.415 Chain T: Q.1 Ligands: NAG-NAG-BMA.34 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.44: 8 residues within 4Å: Chain F: Q.1 Chain V: S.179, E.181, N.232, N.346, V.414, S.415 Ligands: NAG-NAG-BMA.51 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.13: 16 residues within 4Å: Chain C: R.103, I.104, G.106, V.107, V.108 Chain D: N.44, N.45, P.60, G.61, S.62 Chain H: T.267, R.296, H.299, N.301, S.381, R.412 7 PLIP interactions: 2 interactions with chain H, 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: H:R.296, H:R.296, C:G.106, D:N.44, D:N.44, D:N.45, D:G.61 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.30: 16 residues within 4Å: Chain K: R.103, I.104, G.106, V.107, V.108 Chain L: N.44, N.45, P.60, G.61, S.62 Chain P: T.267, R.296, H.299, N.301, S.381, R.412 7 PLIP interactions: 1 interactions with chain K, 2 interactions with chain P, 4 interactions with chain L Hydrogen bonds: K:G.106, P:R.296, P:R.296, L:N.44, L:N.44, L:N.45, L:G.61 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.47: 16 residues within 4Å: Chain Q: R.103, I.104, G.106, V.107, V.108 Chain R: N.44, N.45, P.60, G.61, S.62 Chain V: T.267, R.296, H.299, N.301, S.381, R.412 7 PLIP interactions: 2 interactions with chain V, 1 interactions with chain Q, 4 interactions with chain R Hydrogen bonds: V:R.296, V:R.296, Q:G.106, R:N.44, R:N.44, R:N.45, R:G.61

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.15: 5 residues within 4Å: Chain H: M.112, N.355, S.357 Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.32: 5 residues within 4Å: Chain P: M.112, N.355, S.357 Ligands: NAG-NAG-BMA.31, NAG-NAG-BMA.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.49: 5 residues within 4Å: Chain V: M.112, N.355, S.357 Ligands: NAG-NAG-BMA.48, NAG-NAG-BMA.50 No protein-ligand interaction detected (PLIP)

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

NAG.52: 3 residues within 4Å: Chain G: N.107, S.109, E.110 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.109, G:S.109 NAG.54: 1 residues within 4Å: Chain H: N.308 No protein-ligand interaction detected (PLIP) NAG.55: 1 residues within 4Å: Chain H: N.324 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.324 NAG.56: 3 residues within 4Å: Chain O: N.107, S.109, E.110 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:S.109, O:S.109 NAG.58: 1 residues within 4Å: Chain P: N.308 No protein-ligand interaction detected (PLIP) NAG.59: 1 residues within 4Å: Chain P: N.324 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.324 NAG.60: 3 residues within 4Å: Chain U: N.107, S.109, E.110 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:S.109, U:S.109 NAG.62: 1 residues within 4Å: Chain V: N.308 No protein-ligand interaction detected (PLIP) NAG.63: 1 residues within 4Å: Chain V: N.324 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:N.324

3 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.53: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) MAN.57: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN.23 No protein-ligand interaction detected (PLIP) MAN.61: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN.40 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, K. et al., Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Nat. Med. (2018)

Release Date

2018-05-16

Peptides

vFP20.01 Heavy Chain: AIW
vFP20.01 Light chain: BJX
PGT122 Heavy chain: CKQ
PGT122 Light Chain: DLR
VRC03 Light Chain: EMS
VRC03 Heavy Chain: FNT
Glycoprotein 41: GOU
Glycoprotein 120: HPV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
h

I
H

W
3

B
l

J
L

X
4

C
M

K
m

Q
7

D
N

L
n

R
8

E
R

M
r

S
6

F
Q

N
q

T
5

G
D

O
d

U
1

H
C

P
c

V
2

vFP20.01 Heavy Chain

vFP20.01 Light chain

PGT122 Heavy chain

PGT122 Light Chain

VRC03 Light Chain

VRC03 Heavy Chain

Glycoprotein 41

Glycoprotein 120

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