SMTL ID : 6mph.1

Cryo-EM structure at 3.8 A resolution of HIV-1 fusion peptide-directed antibody, DF1W-a.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 3.80 Å

Oligo State

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

Ligands

8 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.1: 12 residues within 4Å: Chain F: T.267, R.296, H.299, N.301, S.381, T.383 Chain Q: R.103, I.104, G.106, V.107, V.108 Chain S: S.62 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain Q Hydrogen bonds: F:R.296, F:R.296, Q:V.108 NAG-NAG-BMA-MAN-MAN.4: 8 residues within 4Å: Chain F: V.104, T.105, N.118, S.120, Y.135, D.290, I.291 Chain S: E.19 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.135 Hydrogen bonds: F:Y.135 NAG-NAG-BMA-MAN-MAN.12: 6 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG-BMA.11, NAG-NAG-BMA.11, NAG-NAG-BMA.13, NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 8 residues within 4Å: Chain G: V.104, T.105, N.118, S.120, Y.135, D.290, I.291 Chain T: E.19 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Y.135 Hydrogen bonds: G:Y.135 NAG-NAG-BMA-MAN-MAN.25: 6 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG-BMA.24, NAG-NAG-BMA.24, NAG-NAG-BMA.26, NAG-NAG-BMA.26 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.27: 13 residues within 4Å: Chain H: N.265, T.267, R.296, H.299, N.301, S.381, T.383 Chain M: R.103, I.104, G.106, V.107, V.108 Chain N: S.62 4 PLIP interactions: 2 interactions with chain M, 2 interactions with chain H Hydrogen bonds: M:Y.105, M:V.108, H:R.296, H:R.296 NAG-NAG-BMA-MAN-MAN.30: 8 residues within 4Å: Chain H: V.104, T.105, N.118, S.120, Y.135, D.290, I.291 Chain N: E.19 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:Y.135 Hydrogen bonds: H:Y.135 NAG-NAG-BMA-MAN-MAN.38: 6 residues within 4Å: Chain H: N.355, S.357 Ligands: NAG-NAG-BMA.37, NAG-NAG-BMA.37, NAG-NAG-BMA.39, NAG-NAG-BMA.39 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 5 residues within 4Å: Chain F: N.103, I.108, D.110, R.113, R.140 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.113 NAG-NAG.6: 4 residues within 4Å: Chain F: R.162, I.164, N.167 Chain H: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain F: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain F: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain G: N.103, I.108, D.110, R.113, R.140 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.113 NAG-NAG.19: 4 residues within 4Å: Chain F: R.278 Chain G: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain G: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain G: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain H: N.103, I.108, D.110, R.113, R.140 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.113 NAG-NAG.32: 3 residues within 4Å: Chain G: R.278 Chain H: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain H: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain H: N.271, I.292 No protein-ligand interaction detected (PLIP)

7 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.3: 8 residues within 4Å: Chain F: N.107, T.109 Chain Q: D.56, N.58, F.114, T.115 Chain S: D.89, T.94 3 PLIP interactions: 3 interactions with chain Q Hydrogen bonds: Q:D.56, Q:D.56, Q:D.56, Q:N.58, Q:T.115 NAG-NAG-BMA-MAN.14: 13 residues within 4Å: Chain G: N.265, T.267, R.296, H.299, N.301, S.381, T.383 Chain R: R.103, I.104, G.106, V.107, V.108 Chain T: S.62 5 PLIP interactions: 2 interactions with chain T, 1 interactions with chain R, 2 interactions with chain G Hydrogen bonds: T:S.62, T:S.62, R:R.103, R:R.103, R:R.103, G:R.296, G:R.296, R:V.108 NAG-NAG-BMA-MAN.16: 8 residues within 4Å: Chain G: N.107, T.109 Chain R: D.56, N.58, F.114, T.115 Chain T: D.89, T.94 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:D.56, R:D.56, R:D.56, R:T.115 NAG-NAG-BMA-MAN.29: 9 residues within 4Å: Chain H: N.107, T.109 Chain M: Y.50, D.56, N.58, F.114, T.115 Chain N: D.89, T.94 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:D.56, M:D.56, M:D.56, M:T.115 NAG-NAG-BMA-MAN.40: 9 residues within 4Å: Chain H: N.64, K.67, T.206, N.246 Chain O: Y.111 Chain P: A.31, D.49, S.51, F.90 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain H Hydrogen bonds: P:S.51, P:D.49 Hydrophobic interactions: H:T.206 NAG-NAG-BMA-MAN.41: 9 residues within 4Å: Chain F: N.64, K.67, T.206, N.246 Chain U: Y.111 Chain W: A.31, D.49, S.51, F.90 3 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W, 1 interactions with chain F Hydrogen bonds: U:Y.111, W:S.51, W:D.49 Hydrophobic interactions: F:T.206 NAG-NAG-BMA-MAN.42: 9 residues within 4Å: Chain G: N.64, K.67, T.206, N.246 Chain V: Y.111 Chain X: A.31, D.49, S.51, F.90 2 PLIP interactions: 1 interactions with chain X, 1 interactions with chain G Hydrogen bonds: X:S.51, X:D.49 Hydrophobic interactions: G:T.206

12 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.5: 6 residues within 4Å: Chain F: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain F: N.204, T.206, N.246, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 8 residues within 4Å: Chain F: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 6 residues within 4Å: Chain F: S.357, N.361 Ligands: NAG-NAG-BMA.11, NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 6 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain G: N.204, T.206, N.246, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 8 residues within 4Å: Chain G: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.25, NAG-NAG-BMA-MAN-MAN.25, NAG-NAG-BMA.26 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 5 residues within 4Å: Chain G: S.357, N.361 Ligands: NAG-NAG-BMA.24, NAG-NAG-BMA-MAN-MAN.25, NAG-NAG-BMA-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 6 residues within 4Å: Chain H: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 4 residues within 4Å: Chain H: N.204, T.206, N.246, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 8 residues within 4Å: Chain H: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.38, NAG-NAG-BMA-MAN-MAN.38, NAG-NAG-BMA.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 5 residues within 4Å: Chain H: S.357, N.361 Ligands: NAG-NAG-BMA.37, NAG-NAG-BMA-MAN-MAN.38, NAG-NAG-BMA-MAN-MAN.38 No protein-ligand interaction detected (PLIP)

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.8: 7 residues within 4Å: Chain F: N.37, S.179, E.181, L.231, N.232, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.21: 7 residues within 4Å: Chain G: N.37, S.179, E.181, L.231, N.232, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.34: 7 residues within 4Å: Chain H: N.37, S.179, E.181, L.231, N.232, V.414, S.415 No protein-ligand interaction detected (PLIP)

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

NAG.43: 1 residues within 4Å: Chain E: N.126 No protein-ligand interaction detected (PLIP) NAG.44: 2 residues within 4Å: Chain F: N.308, S.362 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.308 NAG.45: 2 residues within 4Å: Chain B: D.33 Chain F: N.58 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:N.58 Hydrophobic interactions: B:D.33 NAG.46: 2 residues within 4Å: Chain G: N.308, S.362 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.308 NAG.47: 2 residues within 4Å: Chain D: D.33 Chain G: N.58 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain J, 1 interactions with chain D Hydrogen bonds: G:N.58, J:Q.119 Hydrophobic interactions: D:D.33 NAG.48: 2 residues within 4Å: Chain H: N.308, S.362 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.308 NAG.49: 3 residues within 4Å: Chain H: N.58 Chain I: T.116 Chain L: D.33 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain H Hydrophobic interactions: L:D.33 Hydrogen bonds: H:N.58 NAG.50: 1 residues within 4Å: Chain I: N.126 No protein-ligand interaction detected (PLIP) NAG.51: 1 residues within 4Å: Chain J: N.126 No protein-ligand interaction detected (PLIP)

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

DF1W-a.01 heavy chain: ACK
DF1W-a.01 Light chain: BDL
Envelope glycoprotein gp41: EIJ
Envelope glycoprotein gp120: FGH
PGT122 heavy chain: MQR
PGT122 Light Chain: NST
VRC03 Heavy chain: OUV
VRC03 Light Chain: PWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

C
3

K
H

B
2

D
4

L
L

E
6

I
D

J
E

F
A

G
B

H
C

M
M

Q
X

R
Y

N
N

S
Z

T
a

O
Q

U
f

V
g

P
R

W
h

X
i

DF1W-a.01 heavy chain

DF1W-a.01 Light chain

Envelope glycoprotein gp41

Envelope glycoprotein gp120

PGT122 heavy chain

PGT122 Light Chain

VRC03 Heavy chain

VRC03 Light Chain

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