SMTL ID : 6mpg.1

Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody, A12V163-b.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

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

Ligands

21 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: 5 residues within 4Å: Chain C: N.103, D.110, M.112, K.159, Y.161 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.112 NAG-NAG.3: 5 residues within 4Å: Chain C: V.104, T.105, N.118, S.120, Y.135 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.135 NAG-NAG.4: 6 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: N.204, T.206, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain C: Q.263, N.265, N.301, V.302, S.303, S.381, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain I: N.103, D.110, M.112, K.159, Y.161 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:M.112 NAG-NAG.17: 5 residues within 4Å: Chain I: V.104, T.105, N.118, S.120, Y.135 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.135 NAG-NAG.18: 6 residues within 4Å: Chain I: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain I: N.204, T.206, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain I: Q.263, N.265, N.301, V.302, S.303, S.381, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain I: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain I: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.20 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain Q: N.103, D.110, M.112, K.159, Y.161 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:M.112 NAG-NAG.31: 5 residues within 4Å: Chain Q: V.104, T.105, N.118, S.120, Y.135 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:Y.135 NAG-NAG.32: 6 residues within 4Å: Chain Q: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain Q: N.204, T.206, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 7 residues within 4Å: Chain Q: Q.263, N.265, N.301, V.302, S.303, S.381, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain Q: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 4 residues within 4Å: Chain Q: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.34 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: 9 residues within 4Å: Chain C: N.107, I.108 Chain E: Y.50, F.114, T.115, F.117 Chain F: W.88, D.89, T.94 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.50, E:T.115 NAG-NAG-BMA-MAN.10: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA.9, NAG.46 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 10 residues within 4Å: Chain C: N.64, K.67, T.206, E.245, N.246 Chain H: N.30, A.31, D.49, S.51, F.90 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: C:T.206 Hydrogen bonds: C:N.64, C:K.67, H:D.49, H:S.51, H:S.51 NAG-NAG-BMA-MAN.16: 9 residues within 4Å: Chain I: N.107, I.108 Chain L: Y.50, F.114, T.115, F.117 Chain M: W.88, D.89, T.94 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:Y.50, L:T.115 NAG-NAG-BMA-MAN.24: 5 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG-NAG-BMA.23, NAG-NAG-BMA.23, NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.27: 10 residues within 4Å: Chain I: N.64, K.67, T.206, E.245, N.246 Chain N: N.30, A.31, D.49, S.51, F.90 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain N Hydrophobic interactions: I:T.206 Hydrogen bonds: I:N.64, I:K.67, N:D.49, N:S.51, N:S.51 NAG-NAG-BMA-MAN.30: 9 residues within 4Å: Chain Q: N.107, I.108 Chain S: Y.50, F.114, T.115, F.117 Chain T: W.88, D.89, T.94 2 PLIP interactions: 2 interactions with chain S Hydrogen bonds: S:Y.50, S:T.115 NAG-NAG-BMA-MAN.38: 5 residues within 4Å: Chain Q: N.355, S.357 Ligands: NAG-NAG-BMA.37, NAG-NAG-BMA.37, NAG.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.41: 10 residues within 4Å: Chain Q: N.64, K.67, T.206, E.245, N.246 Chain V: N.30, A.31, D.49, S.51, F.90 5 PLIP interactions: 3 interactions with chain Q, 2 interactions with chain V Hydrophobic interactions: Q:T.206 Hydrogen bonds: Q:N.64, Q:K.67, V:D.49, V:S.51, V:S.51

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: 7 residues within 4Å: Chain C: P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.20: 7 residues within 4Å: Chain I: P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.34: 7 residues within 4Å: Chain Q: P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.40 No protein-ligand interaction detected (PLIP)

6 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.9: 8 residues within 4Å: Chain C: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN.10, NAG-NAG-BMA-MAN.10, NAG.46 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 6 residues within 4Å: Chain B: T.18 Chain C: N.58 Chain D: G.55, I.56, T.57, F.70 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.56 Hydrogen bonds: D:G.55, D:G.55 NAG-NAG-BMA.23: 8 residues within 4Å: Chain I: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN.24, NAG-NAG-BMA-MAN.24, NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 6 residues within 4Å: Chain I: N.58 Chain J: G.55, I.56, T.57, F.70 Chain P: T.18 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:I.56 Hydrogen bonds: J:G.55, J:G.55 NAG-NAG-BMA.37: 8 residues within 4Å: Chain Q: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN.38, NAG-NAG-BMA-MAN.38, NAG.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 6 residues within 4Å: Chain Q: N.58 Chain R: T.18 Chain W: G.55, I.56, T.57, F.70 3 PLIP interactions: 3 interactions with chain W Hydrophobic interactions: W:I.56 Hydrogen bonds: W:G.55, W:G.55

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.11: 17 residues within 4Å: Chain C: T.267, R.296, H.299, N.301, S.381, T.383 Chain E: R.103, I.104, G.106, V.107 Chain F: S.24, N.44, N.45, N.46, P.60, G.61, S.62 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.106, E:V.108, C:R.296, C:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.25: 17 residues within 4Å: Chain I: T.267, R.296, H.299, N.301, S.381, T.383 Chain L: R.103, I.104, G.106, V.107 Chain M: S.24, N.44, N.45, N.46, P.60, G.61, S.62 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain I Hydrogen bonds: L:G.106, L:V.108, I:R.296, I:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.39: 17 residues within 4Å: Chain Q: T.267, R.296, H.299, N.301, S.381, T.383 Chain S: R.103, I.104, G.106, V.107 Chain T: S.24, N.44, N.45, N.46, P.60, G.61, S.62 4 PLIP interactions: 2 interactions with chain S, 2 interactions with chain Q Hydrogen bonds: S:G.106, S:V.108, Q:R.296, Q:R.296

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

NAG.43: 3 residues within 4Å: Chain B: E.123, N.126, Y.127 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.127 NAG.44: 3 residues within 4Å: Chain C: R.162, N.167 Chain I: R.278 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain C Hydrogen bonds: I:R.278, C:R.162 NAG.45: 1 residues within 4Å: Chain C: N.324 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.324 NAG.46: 5 residues within 4Å: Chain C: S.357, N.361 Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA-MAN.10, NAG-NAG-BMA-MAN.10 No protein-ligand interaction detected (PLIP) NAG.47: 3 residues within 4Å: Chain I: R.162, N.167 Chain Q: R.278 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain Q Hydrogen bonds: I:R.162, Q:R.278 NAG.48: 1 residues within 4Å: Chain I: N.324 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.324 NAG.49: 5 residues within 4Å: Chain I: S.357, N.361 Ligands: NAG-NAG-BMA.23, NAG-NAG-BMA-MAN.24, NAG-NAG-BMA-MAN.24 No protein-ligand interaction detected (PLIP) NAG.50: 3 residues within 4Å: Chain P: E.123, N.126, Y.127 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:Y.127 NAG.51: 3 residues within 4Å: Chain C: R.278 Chain Q: R.162, N.167 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain Q Hydrogen bonds: C:R.278, Q:R.162 NAG.52: 1 residues within 4Å: Chain Q: N.324 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.324 NAG.53: 5 residues within 4Å: Chain Q: S.357, N.361 Ligands: NAG-NAG-BMA.37, NAG-NAG-BMA-MAN.38, NAG-NAG-BMA-MAN.38 No protein-ligand interaction detected (PLIP) NAG.54: 3 residues within 4Å: Chain R: E.123, N.126, Y.127 1 PLIP interactions: 1 interactions with chain R Hydrophobic interactions: R:Y.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kong, R. et al., Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization. Cell (2019)

Release Date

2019-07-24

Peptides

A12V163-b.01 Light Chain: AKX
Envelope glycoprotein gp41: BPR
Envelope glycoprotein gp120: CIQ
A12V163-b.01 Heavy Chain: DJW
PGT122 Heavy chain: ELS
PGT122 Light chain: FMT
VRC03 heavy chain: GOU
VRC03 Light chain: HNV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

K
4

X
Y

B
U

P
A

R
D

C
V

I
2

Q
C

D
W

J
3

W
X

E
m

L
5

S
M

F
n

M
6

T
N

G
q

O
8

U
Q

H
r

N
7

V
R

A12V163-b.01 Light Chain

Envelope glycoprotein gp41

Envelope glycoprotein gp120

A12V163-b.01 Heavy Chain

PGT122 Heavy chain

PGT122 Light chain

VRC03 heavy chain

VRC03 Light chain

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