SMTL ID : 6cdi.1

Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 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: 4 residues within 4Å: Chain A: N.100, S.102, L.134 Chain O: R.100 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:R.100 NAG-NAG-BMA.8: 3 residues within 4Å: Chain B: N.204, T.206, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 6 residues within 4Å: Chain B: N.332, S.333, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN.13, NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain I: N.100, S.102, L.134 Chain W: R.100 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:R.100 NAG-NAG-BMA.25: 3 residues within 4Å: Chain J: N.204, T.206, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 6 residues within 4Å: Chain J: N.332, S.333, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.30, NAG-NAG-BMA-MAN-MAN.30, NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 4 residues within 4Å: Chain G: R.100 Chain Q: N.100, S.102, L.134 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.100, G:R.100 NAG-NAG-BMA.42: 3 residues within 4Å: Chain R: N.204, T.206, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.46: 6 residues within 4Å: Chain R: N.332, S.333, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.47, NAG-NAG-BMA-MAN-MAN.47, NAG-NAG.48 No protein-ligand interaction detected (PLIP)

9 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 A: S.17, T.18, A.21, D.113 Chain B: N.58 Chain G: G.56, A.57, S.58, T.71, A.72, D.73 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain G Hydrogen bonds: A:T.18, G:G.56, G:G.56, G:T.71, G:T.71, G:D.73 NAG-NAG-BMA-MAN.4: 10 residues within 4Å: Chain B: N.107, I.108, T.109 Chain C: W.88, D.89, T.94 Chain D: D.56, N.58, F.114, T.115 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.56, D:N.58, D:T.115 NAG-NAG-BMA-MAN.17: 8 residues within 4Å: Chain B: K.67, T.206, E.245, N.246 Chain E: A.31, D.49, S.51, F.90 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:R.52, B:K.67, E:D.49, E:S.51 Hydrophobic interactions: B:T.206 NAG-NAG-BMA-MAN.19: 11 residues within 4Å: Chain I: S.17, T.18, A.21, D.113 Chain J: N.58 Chain O: G.56, A.57, S.58, T.71, A.72, D.73 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain O Hydrogen bonds: I:T.18, O:G.56, O:G.56, O:T.71, O:T.71, O:D.73 NAG-NAG-BMA-MAN.21: 10 residues within 4Å: Chain J: N.107, I.108, T.109 Chain K: W.88, D.89, T.94 Chain L: D.56, N.58, F.114, T.115 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:D.56, L:N.58, L:T.115 NAG-NAG-BMA-MAN.34: 8 residues within 4Å: Chain J: K.67, T.206, E.245, N.246 Chain M: A.31, D.49, S.51, F.90 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain J Hydrogen bonds: M:R.52, J:K.67, M:D.49, M:S.51 Hydrophobic interactions: J:T.206 NAG-NAG-BMA-MAN.36: 11 residues within 4Å: Chain Q: S.17, T.18, A.21, D.113 Chain R: N.58 Chain W: G.56, A.57, S.58, T.71, A.72, D.73 4 PLIP interactions: 3 interactions with chain W, 1 interactions with chain Q Hydrogen bonds: W:G.56, W:G.56, Q:T.18, W:T.71, W:T.71, W:D.73 NAG-NAG-BMA-MAN.38: 10 residues within 4Å: Chain R: N.107, I.108, T.109 Chain S: W.88, D.89, T.94 Chain T: D.56, N.58, F.114, T.115 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:D.56, T:N.58, T:T.115 NAG-NAG-BMA-MAN.51: 8 residues within 4Å: Chain R: K.67, T.206, E.245, N.246 Chain U: A.31, D.49, S.51, F.90 3 PLIP interactions: 1 interactions with chain U, 2 interactions with chain R Hydrogen bonds: U:R.52, R:K.67, U:D.49, U:S.51 Hydrophobic interactions: R:T.206

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.3: 6 residues within 4Å: Chain B: N.103, D.110, M.112, K.117, R.140, K.159 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.112 NAG-NAG.10: 4 residues within 4Å: Chain B: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: S.357, N.361 Ligands: NAG-NAG-BMA.12, NAG-NAG-BMA-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: P.261, V.414, N.416 Chain H: D.75 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain J: N.103, D.110, M.112, K.117, R.140, K.159 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:M.112 NAG-NAG.27: 4 residues within 4Å: Chain J: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain J: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 5 residues within 4Å: Chain J: S.357, N.361 Ligands: NAG-NAG-BMA.29, NAG-NAG-BMA-MAN-MAN.30, NAG-NAG-BMA-MAN-MAN.30 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain J: P.261, V.414, N.416 Chain P: D.75 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 6 residues within 4Å: Chain R: N.103, D.110, M.112, K.117, R.140, K.159 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:M.112 NAG-NAG.44: 4 residues within 4Å: Chain R: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 3 residues within 4Å: Chain R: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 5 residues within 4Å: Chain R: S.357, N.361 Ligands: NAG-NAG-BMA.46, NAG-NAG-BMA-MAN-MAN.47, NAG-NAG-BMA-MAN-MAN.47 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 4 residues within 4Å: Chain R: P.261, V.414, N.416 Chain X: D.75 No protein-ligand interaction detected (PLIP)

6 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.5: 5 residues within 4Å: Chain B: V.104, T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 5 residues within 4Å: Chain B: N.355, S.357 Ligands: NAG-NAG-BMA.12, NAG-NAG-BMA.12, NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 5 residues within 4Å: Chain J: V.104, T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.30: 5 residues within 4Å: Chain J: N.355, S.357 Ligands: NAG-NAG-BMA.29, NAG-NAG-BMA.29, NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.39: 5 residues within 4Å: Chain R: V.104, T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.47: 5 residues within 4Å: Chain R: N.355, S.357 Ligands: NAG-NAG-BMA.46, NAG-NAG-BMA.46, NAG-NAG.48 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.6: 5 residues within 4Å: Chain B: Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.23: 5 residues within 4Å: Chain J: Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.40: 5 residues within 4Å: Chain R: Q.100, S.120, N.122, K.131, K.133 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.7: 4 residues within 4Å: Chain B: R.162, N.167 Chain F: K.19 Chain J: R.278 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.19, F:K.19 NAG-NAG-BMA-MAN.24: 4 residues within 4Å: Chain J: R.162, N.167 Chain N: K.19 Chain R: R.278 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:K.19, N:K.19 NAG-NAG-BMA-MAN.41: 4 residues within 4Å: Chain B: R.278 Chain R: R.162, N.167 Chain V: K.19 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:K.19, V:K.19

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.9: 10 residues within 4Å: Chain B: S.179, E.181, P.182, L.231, N.232, R.274, N.346, G.348, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.26: 10 residues within 4Å: Chain J: S.179, E.181, P.182, L.231, N.232, R.274, N.346, G.348, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.43: 10 residues within 4Å: Chain R: S.179, E.181, P.182, L.231, N.232, R.274, N.346, G.348, V.414, S.415 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-(1-2)-alpha-D-mannopyranose-(1-3)-[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.15: 17 residues within 4Å: Chain B: T.267, R.296, H.299, N.301, S.381, T.383 Chain C: S.24, N.44, N.45, P.60, G.61, S.62 Chain D: R.103, I.104, G.106, V.107, V.108 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:V.108 Hydrogen bonds: D:V.108, B:R.296, B:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.32: 17 residues within 4Å: Chain J: T.267, R.296, H.299, N.301, S.381, T.383 Chain K: S.24, N.44, N.45, P.60, G.61, S.62 Chain L: R.103, I.104, G.106, V.107, V.108 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: L:V.108 Hydrogen bonds: L:V.108, J:R.296, J:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.49: 17 residues within 4Å: Chain R: T.267, R.296, H.299, N.301, S.381, T.383 Chain S: S.24, N.44, N.45, P.60, G.61, S.62 Chain T: R.103, I.104, G.106, V.107, V.108 4 PLIP interactions: 2 interactions with chain T, 2 interactions with chain R Hydrophobic interactions: T:V.108 Hydrogen bonds: T:V.108, R:R.296, R:R.296

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

NAG.52: 2 residues within 4Å: Chain A: K.122, N.126 No protein-ligand interaction detected (PLIP) NAG.53: 1 residues within 4Å: Chain B: N.324 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.316, B:K.316, B:N.324 NAG.54: 2 residues within 4Å: Chain I: K.122, N.126 No protein-ligand interaction detected (PLIP) NAG.55: 1 residues within 4Å: Chain J: N.324 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:K.316, J:K.316, J:N.324 NAG.56: 2 residues within 4Å: Chain Q: K.122, N.126 No protein-ligand interaction detected (PLIP) NAG.57: 1 residues within 4Å: Chain R: N.324 3 PLIP interactions: 3 interactions with chain R Hydrogen bonds: R:K.316, R:K.316, R:N.324

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

Glycoprotein gp41: AIQ
Glycoprotein 120: BJR
PGT122 Light Chain: CKS
PGT122 Heavy Chain: DLT
VRC03 light chain: EMU
VRC03 Heavy Chain: FNV
vFP16.02 Heavy Chain: GOW
vFP16.02 Light Chain: HPX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
c

I
A

Q
D

B
d

J
2

R
C

C
n

K
6

S
N

D
m

L
5

T
M

E
r

M
7

U
R

F
q

N
8

V
Q

G
h

O
3

W
H

H
l

P
4

X
L

Glycoprotein gp41

Glycoprotein 120

PGT122 Light Chain

PGT122 Heavy Chain

VRC03 light chain

VRC03 Heavy Chain

vFP16.02 Heavy Chain

vFP16.02 Light Chain

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