SMTL ID : 6nf2.1

Cryo-EM structure of vaccine-elicited antibody 0PV-c.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

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.1: 2 residues within 4Å: Chain A: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.103, I.108, D.110, R.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.110, A:R.140 NAG-NAG.9: 5 residues within 4Å: Chain A: Q.263, N.265, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: N.271, T.273, I.292, Q.408 Chain K: F.64 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain G: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: N.103, I.108, D.110, R.140 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.110, G:R.140 NAG-NAG.25: 5 residues within 4Å: Chain G: Q.263, N.265, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain F: F.64 Chain G: N.271, T.273, I.292, Q.408 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain G: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.28, NAG-NAG-BMA-MAN-MAN.28 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 2 residues within 4Å: Chain Q: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 4 residues within 4Å: Chain Q: N.103, I.108, D.110, R.140 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:D.110, Q:R.140 NAG-NAG.41: 5 residues within 4Å: Chain Q: Q.263, N.265, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 5 residues within 4Å: Chain Q: N.271, T.273, I.292, Q.408 Chain T: F.64 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 4 residues within 4Å: Chain Q: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.44, NAG-NAG-BMA-MAN-MAN.44 No protein-ligand interaction detected (PLIP)

6 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: 10 residues within 4Å: Chain A: N.107, I.108, T.109 Chain J: G.55, D.56, N.58, F.114, T.115 Chain K: D.89, T.94 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.58, J:T.115, J:D.56, J:D.56, J:G.55 NAG-NAG-BMA-MAN.16: 11 residues within 4Å: Chain A: K.67, T.206, E.245, N.246 Chain M: N.30, A.31, D.49, S.51, R.52, F.90 Chain N: Y.111 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain M Hydrophobic interactions: A:T.206 Hydrogen bonds: A:K.67, M:D.49, M:R.52, M:S.51 NAG-NAG-BMA-MAN.19: 9 residues within 4Å: Chain E: G.55, D.56, N.58, T.115 Chain F: D.89, T.94 Chain G: N.107, I.108, T.109 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.58, E:T.115, E:D.56, E:D.56, E:G.55 NAG-NAG-BMA-MAN.32: 11 residues within 4Å: Chain C: Y.111 Chain D: N.30, A.31, D.49, S.51, R.52, F.90 Chain G: K.67, T.206, E.245, N.246 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:D.49, D:R.52, G:K.67, D:S.51 Hydrophobic interactions: G:T.206 NAG-NAG-BMA-MAN.35: 9 residues within 4Å: Chain Q: N.107, I.108, T.109 Chain S: G.55, D.56, N.58, T.115 Chain T: D.89, T.94 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:N.58, S:T.115, S:D.56, S:D.56, S:G.55 NAG-NAG-BMA-MAN.48: 11 residues within 4Å: Chain Q: K.67, T.206, E.245, N.246 Chain U: N.30, A.31, D.49, S.51, R.52, F.90 Chain V: Y.111 3 PLIP interactions: 1 interactions with chain U, 2 interactions with chain Q Hydrogen bonds: U:D.49, U:R.52, Q:K.67, U:S.51 Hydrophobic interactions: Q:T.206

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: 7 residues within 4Å: Chain A: V.104, T.105, N.118, Y.135, L.137, D.290 Chain K: E.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.135 Hydrogen bonds: A:Y.135 NAG-NAG-BMA-MAN-MAN.12: 4 residues within 4Å: Chain A: N.355 Ligands: NAG-NAG-BMA.11, NAG-NAG-BMA.11, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.20: 7 residues within 4Å: Chain F: E.19 Chain G: V.104, T.105, N.118, Y.135, L.137, D.290 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Y.135 Hydrogen bonds: G:Y.135 NAG-NAG-BMA-MAN-MAN.28: 4 residues within 4Å: Chain G: N.355 Ligands: NAG-NAG-BMA.27, NAG-NAG-BMA.27, NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.36: 7 residues within 4Å: Chain Q: V.104, T.105, N.118, Y.135, L.137, D.290 Chain T: E.19 2 PLIP interactions: 2 interactions with chain Q Hydrophobic interactions: Q:Y.135 Hydrogen bonds: Q:Y.135 NAG-NAG-BMA-MAN-MAN.44: 4 residues within 4Å: Chain Q: N.355 Ligands: NAG-NAG-BMA.43, NAG-NAG-BMA.43, NAG-NAG.45 No protein-ligand interaction detected (PLIP)

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: 5 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain A: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 5 residues within 4Å: Chain A: R.113, N.332, S.333 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.15: 2 residues within 4Å: Chain A: Q.263, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 5 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 3 residues within 4Å: Chain G: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 5 residues within 4Å: Chain G: R.113, N.332, S.333 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.31: 2 residues within 4Å: Chain G: Q.263, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 5 residues within 4Å: Chain Q: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 3 residues within 4Å: Chain Q: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 5 residues within 4Å: Chain Q: R.113, N.332, S.333 Ligands: NAG-NAG-BMA-MAN-MAN.44, NAG-NAG-BMA-MAN-MAN.44 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:R.113 NAG-NAG-BMA.47: 2 residues within 4Å: Chain Q: Q.263, N.416 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.6: 4 residues within 4Å: Chain A: R.162, N.167 Chain N: K.19, Q.76 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:K.19, N:K.19 NAG-NAG-BMA-MAN.22: 4 residues within 4Å: Chain C: K.19, Q.76 Chain G: R.162, N.167 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.19, C:K.19 NAG-NAG-BMA-MAN.38: 4 residues within 4Å: Chain Q: R.162, N.167 Chain V: K.19, Q.76 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.8: 8 residues within 4Å: Chain A: E.181, P.182, N.232, R.274, N.346, G.348, V.414, S.415 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN-MAN.24: 8 residues within 4Å: Chain G: E.181, P.182, N.232, R.274, N.346, G.348, V.414, S.415 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.348 NAG-NAG-BMA-MAN-MAN-MAN.40: 8 residues within 4Å: Chain Q: E.181, P.182, N.232, R.274, N.346, G.348, V.414, S.415 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:G.348

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: 16 residues within 4Å: Chain A: T.267, H.299, N.301, T.383, R.412 Chain J: R.103, I.104, G.106, V.108 Chain K: S.24, N.44, N.45, N.46, P.60, G.61, S.62 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.30: 16 residues within 4Å: Chain E: R.103, I.104, G.106, V.108 Chain F: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain G: T.267, H.299, N.301, T.383, R.412 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.108 Hydrogen bonds: E:G.106 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.46: 16 residues within 4Å: Chain Q: T.267, H.299, N.301, T.383, R.412 Chain S: R.103, I.104, G.106, V.108 Chain T: S.24, N.44, N.45, N.46, P.60, G.61, S.62 1 PLIP interactions: 1 interactions with chain S Hydrophobic interactions: S:V.108

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

NAG.49: 1 residues within 4Å: Chain A: N.324 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.324 NAG.50: 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.51: 2 residues within 4Å: Chain B: N.100, S.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.102 NAG.52: 1 residues within 4Å: Chain G: N.324 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.324 NAG.53: 3 residues within 4Å: Chain I: E.123, N.126, Y.127 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.127 NAG.54: 2 residues within 4Å: Chain I: N.100, S.102 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.102 NAG.55: 1 residues within 4Å: Chain Q: N.324 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.324 NAG.56: 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 NAG.57: 2 residues within 4Å: Chain R: N.100, S.102 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:S.102

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

Envelope glycoprotein gp120: AGQ
Envelope glycoprotein gp41: BIR
VRC03 Heavy Chain: CNV
VRC03 Light Chain: DMU
PGT122 Heavy Chain: EJS
PGT122 Light Chain: FKT
0PV-c.01 Heavy Chain: HOW
0PV-c.01 Light Chain: LPX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
G

Q
Q

B
B

I
I

R
R

C
C

N
N

V
V

D
D

M
M

U
U

E
E

J
J

S
S

F
F

K
K

T
T

H
H

O
O

W
W

L
L

P
P

X
X

Envelope glycoprotein gp120

Envelope glycoprotein gp41

VRC03 Heavy Chain

VRC03 Light Chain

PGT122 Heavy Chain

PGT122 Light Chain

0PV-c.01 Heavy Chain

0PV-c.01 Light Chain

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