SMTL ID : 6ot1.1

Cryo-EM structure of vaccine-elicited antibody 0PV-b.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

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: 4 residues within 4Å: Chain A: S.17 Chain B: E.57, N.58 Chain C: D.57 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.204, S.244, E.245, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain I: S.17 Chain J: E.57, N.58 Chain K: D.57 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain J: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain J: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain J: N.204, S.244, E.245, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain J: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain J: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain J: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.22 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain Q: S.17 Chain R: E.57, N.58 Chain S: D.57 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain R: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 2 residues within 4Å: Chain R: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 4 residues within 4Å: Chain R: N.204, S.244, E.245, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain R: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain R: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 4 residues within 4Å: Chain R: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.37 No protein-ligand interaction detected (PLIP)

9 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.2: 13 residues within 4Å: Chain B: N.107, T.109 Chain E: Y.33, S.54, G.55, D.56, N.58, R.102, F.114, T.115 Chain F: D.89, P.93, T.94 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.58, E:T.115, E:T.115 NAG-NAG-BMA-MAN-MAN.12: 7 residues within 4Å: Chain B: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.11, NAG-NAG-BMA.11, NAG-NAG-BMA.11, NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 7 residues within 4Å: Chain B: T.206, N.246 Chain H: N.30, D.49, T.50, S.51, F.90 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:D.49 Hydrophobic interactions: B:T.206 NAG-NAG-BMA-MAN-MAN.17: 13 residues within 4Å: Chain J: N.107, T.109 Chain M: Y.33, S.54, G.55, D.56, N.58, R.102, F.114, T.115 Chain N: D.89, P.93, T.94 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:N.58, M:T.115, M:T.115 NAG-NAG-BMA-MAN-MAN.27: 7 residues within 4Å: Chain J: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.26, NAG-NAG-BMA.26, NAG-NAG-BMA.26, NAG-NAG-BMA.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.30: 7 residues within 4Å: Chain J: T.206, N.246 Chain P: N.30, D.49, T.50, S.51, F.90 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain P Hydrophobic interactions: J:T.206 Hydrogen bonds: P:D.49 NAG-NAG-BMA-MAN-MAN.32: 13 residues within 4Å: Chain R: N.107, T.109 Chain U: Y.33, S.54, G.55, D.56, N.58, R.102, F.114, T.115 Chain V: D.89, P.93, T.94 3 PLIP interactions: 3 interactions with chain U Hydrogen bonds: U:N.58, U:T.115, U:T.115 NAG-NAG-BMA-MAN-MAN.42: 7 residues within 4Å: Chain R: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.41, NAG-NAG-BMA.41, NAG-NAG-BMA.41, NAG-NAG-BMA.43 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.45: 7 residues within 4Å: Chain R: T.206, N.246 Chain X: N.30, D.49, T.50, S.51, F.90 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain X Hydrophobic interactions: R:T.206 Hydrogen bonds: X:D.49

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.3: 6 residues within 4Å: Chain B: V.104, T.105, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 6 residues within 4Å: Chain B: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain B: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 6 residues within 4Å: Chain J: V.104, T.105, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 6 residues within 4Å: Chain J: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.27, NAG-NAG-BMA-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 3 residues within 4Å: Chain J: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 6 residues within 4Å: Chain R: V.104, T.105, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 6 residues within 4Å: Chain R: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.42, NAG-NAG-BMA-MAN-MAN.42 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 3 residues within 4Å: Chain R: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.42 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.7: 8 residues within 4Å: Chain B: E.181, P.182, L.231, N.232, N.346, V.414, S.415 Ligands: NAG-NAG.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.181 NAG-NAG-BMA-MAN.22: 8 residues within 4Å: Chain J: E.181, P.182, L.231, N.232, N.346, V.414, S.415 Ligands: NAG-NAG.29 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.181 NAG-NAG-BMA-MAN.37: 8 residues within 4Å: Chain R: E.181, P.182, L.231, N.232, N.346, V.414, S.415 Ligands: NAG-NAG.44 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:E.181

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.10: 17 residues within 4Å: Chain B: N.265, T.267, R.296, H.299, N.301, T.383 Chain E: R.103, I.104, G.106, V.107, V.108 Chain F: S.24, N.44, N.45, P.60, G.61, S.62 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:R.296, E:V.108 NAG-NAG-BMA-MAN-MAN-MAN.25: 17 residues within 4Å: Chain J: N.265, T.267, R.296, H.299, N.301, T.383 Chain M: R.103, I.104, G.106, V.107, V.108 Chain N: S.24, N.44, N.45, P.60, G.61, S.62 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain J Hydrogen bonds: M:V.108, J:R.296 NAG-NAG-BMA-MAN-MAN-MAN.40: 17 residues within 4Å: Chain R: N.265, T.267, R.296, H.299, N.301, T.383 Chain U: R.103, I.104, G.106, V.107, V.108 Chain V: S.24, N.44, N.45, P.60, G.61, S.62 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain U Hydrogen bonds: R:R.296, U:V.108

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

NAG.46: 3 residues within 4Å: Chain A: K.122, N.126 Chain L: S.57 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain A Hydrogen bonds: L:S.57, L:S.57, A:N.126 NAG.47: 3 residues within 4Å: Chain B: N.103, I.108, R.140 No protein-ligand interaction detected (PLIP) NAG.48: 1 residues within 4Å: Chain B: N.308 No protein-ligand interaction detected (PLIP) NAG.49: 1 residues within 4Å: Chain B: N.324 No protein-ligand interaction detected (PLIP) NAG.50: 3 residues within 4Å: Chain I: K.122, N.126 Chain T: S.57 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain T Hydrogen bonds: I:N.126, T:S.57, T:S.57 NAG.51: 3 residues within 4Å: Chain J: N.103, I.108, R.140 No protein-ligand interaction detected (PLIP) NAG.52: 1 residues within 4Å: Chain J: N.308 No protein-ligand interaction detected (PLIP) NAG.53: 1 residues within 4Å: Chain J: N.324 No protein-ligand interaction detected (PLIP) NAG.54: 3 residues within 4Å: Chain D: S.57 Chain Q: K.122, N.126 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain Q Hydrogen bonds: D:S.57, D:S.57, Q:N.126 NAG.55: 3 residues within 4Å: Chain R: N.103, I.108, R.140 No protein-ligand interaction detected (PLIP) NAG.56: 1 residues within 4Å: Chain R: N.308 No protein-ligand interaction detected (PLIP) NAG.57: 1 residues within 4Å: Chain R: N.324 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

2019-08-07

Peptides

Envelope glycoprotein gp41: AIQ
BG505 gp120: BJR
0PV-b.01 heavy: CKS
0PV-b.01 light: DLT
PGT122 heavy: EMU
PGT122 light: FNV
VRC03 heavy: GOW
VRC03 light: HPX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

I
O

Q
D

B
G

J
E

R
P

C
H

K
A

S
M

D
L

L
C

T
N

E
m

M
F

U
Q

F
n

N
I

V
R

G
q

O
J

W
S

H
r

P
K

X
T

Envelope glycoprotein gp41

BG505 gp120

0PV-b.01 heavy

0PV-b.01 light

PGT122 heavy

PGT122 light

VRC03 heavy

VRC03 light

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