SMTL ID : 6osy.1

Cryo-EM structure of vaccine-elicited antibody 0PV-a.01 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- 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.1: 3 residues within 4Å: Chain A: N.58 Chain Q: N.31, Y.67 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.31 NAG-NAG-BMA-MAN.3: 12 residues within 4Å: Chain A: N.107, I.108, T.109 Chain B: G.55, D.56, N.58, F.114, T.115 Chain C: D.89, R.92, P.93, T.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.56, B:G.55, B:N.58, B:T.115 NAG-NAG-BMA-MAN.16: 6 residues within 4Å: Chain A: N.246 Chain D: G.29, A.31, S.66, G.67, F.90 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.67, D:G.67 NAG-NAG-BMA-MAN.17: 3 residues within 4Å: Chain G: N.58 Chain O: N.31, Y.67 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:N.31 NAG-NAG-BMA-MAN.19: 11 residues within 4Å: Chain G: N.107, I.108, T.109 Chain H: G.55, D.56, N.58, T.115 Chain I: D.89, R.92, P.93, T.94 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:D.56, H:G.55, H:N.58, H:T.115 NAG-NAG-BMA-MAN.32: 6 residues within 4Å: Chain G: N.246 Chain J: G.29, A.31, S.66, G.67, F.90 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:S.66, J:S.66, J:G.67 NAG-NAG-BMA-MAN.33: 3 residues within 4Å: Chain P: N.58 Chain X: N.31, Y.67 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:N.31 NAG-NAG-BMA-MAN.35: 11 residues within 4Å: Chain P: N.107, I.108, T.109 Chain R: G.55, D.56, N.58, T.115 Chain S: D.89, R.92, P.93, T.94 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:D.56, R:G.55, R:N.58, R:T.115 NAG-NAG-BMA-MAN.48: 6 residues within 4Å: Chain P: N.246 Chain T: G.29, N.30, A.31, S.66, G.67 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:G.67, T:G.67

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.103, K.117, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: N.271, I.292 Chain C: F.64 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain A: G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain G: N.103, K.117, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 1 residues within 4Å: Chain G: N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain G: N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain G: N.271, I.292 Chain I: F.64 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain G: G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain P: N.103, K.117, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 1 residues within 4Å: Chain P: N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain P: N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 3 residues within 4Å: Chain P: N.271, I.292 Chain S: F.64 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 2 residues within 4Å: Chain P: G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 4 residues within 4Å: Chain P: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.40 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.4: 8 residues within 4Å: Chain A: V.104, T.105, N.118, S.120, Y.135, L.137, D.290 Chain C: E.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.12: 5 residues within 4Å: Chain A: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.11, NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.20: 7 residues within 4Å: Chain G: V.104, T.105, N.118, Y.135, L.137, D.290 Chain I: E.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.28: 5 residues within 4Å: Chain G: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.27, NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.36: 7 residues within 4Å: Chain P: V.104, T.105, N.118, S.120, Y.135, D.290 Chain S: E.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.44: 5 residues within 4Å: Chain P: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.43, NAG-NAG-BMA.43 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.5: 5 residues within 4Å: Chain A: Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 7 residues within 4Å: Chain A: R.113, N.332, S.333, T.341, N.355 Ligands: NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.113 NAG-NAG-BMA.21: 5 residues within 4Å: Chain G: Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 7 residues within 4Å: Chain G: R.113, N.332, S.333, T.341, N.355 Ligands: NAG-NAG-BMA-MAN-MAN.28, NAG-NAG-BMA-MAN-MAN.28 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.113 NAG-NAG-BMA.37: 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.43: 7 residues within 4Å: Chain P: R.113, N.332, S.333, T.341, N.355 Ligands: NAG-NAG-BMA-MAN-MAN.44, NAG-NAG-BMA-MAN-MAN.44 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:R.113

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.6: 6 residues within 4Å: Chain A: V.144, R.162, I.164, N.167 Chain E: K.19, Q.76 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.164 NAG-NAG-BMA-MAN.22: 5 residues within 4Å: Chain G: R.162, I.164, N.167 Chain K: K.19, Q.76 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:I.164 NAG-NAG-BMA-MAN.38: 4 residues within 4Å: Chain P: R.162, I.164, N.167 Chain U: Q.76 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:I.164

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: 10 residues within 4Å: Chain A: E.181, P.182, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.24: 10 residues within 4Å: Chain G: E.181, P.182, V.224, L.231, N.232, N.346, I.407, V.414, S.415 Ligands: NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.40: 10 residues within 4Å: Chain P: E.181, V.224, L.231, N.232, N.346, G.348, I.407, V.414, S.415 Ligands: NAG-NAG.47 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.14: 13 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, T.383 Chain B: R.103, I.104, G.106, V.108 Chain C: N.44, N.45, N.46, S.62 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.296 Hydrophobic interactions: B:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.30: 14 residues within 4Å: Chain G: T.267, R.296, H.299, N.301, T.383 Chain H: R.103, I.104, G.106, V.108 Chain I: N.44, N.45, N.46, G.61, S.62 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:V.108 Hydrogen bonds: G:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.46: 13 residues within 4Å: Chain P: T.267, R.296, H.299, N.301, T.383 Chain R: R.103, I.104, G.106, V.108 Chain S: N.44, N.45, N.46, S.62 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain P Hydrophobic interactions: R:V.108 Hydrogen bonds: P:R.296

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

NAG.49: 1 residues within 4Å: Chain A: N.324 No protein-ligand interaction detected (PLIP) NAG.50: 1 residues within 4Å: Chain F: N.126 No protein-ligand interaction detected (PLIP) NAG.51: 2 residues within 4Å: Chain F: N.100 Chain N: P.64 No protein-ligand interaction detected (PLIP) NAG.52: 1 residues within 4Å: Chain G: N.324 No protein-ligand interaction detected (PLIP) NAG.53: 1 residues within 4Å: Chain L: N.126 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:S.87 NAG.54: 2 residues within 4Å: Chain L: N.100 Chain W: P.64 No protein-ligand interaction detected (PLIP) NAG.55: 1 residues within 4Å: Chain P: N.324 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.324 NAG.56: 1 residues within 4Å: Chain V: N.126 No protein-ligand interaction detected (PLIP) NAG.57: 3 residues within 4Å: Chain M: P.64 Chain V: N.100, S.101 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

BG505 gp120: AGP
PGT122 Heavy: BHR
PGT122 Light: CIS
VRC03 Light: DJT
VRC03 Heavy: EKU
BG505 gp41: FLV
0PV-a.01 Heavy: MNW
0PV-a.01 Light: OQX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

G
B

P
K

B
5

H
C

R
M

C
6

I
D

S
N

D
7

J
E

T
O

E
8

K
F

U
P

F
A

L
G

V
Q

M
H

N
I

W
R

O
J

Q
L

X
S

BG505 gp120

PGT122 Heavy

PGT122 Light

VRC03 Light

VRC03 Heavy

BG505 gp41

0PV-a.01 Heavy

0PV-a.01 Light

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