SMTL ID : 6n1v.1

Cryo-EM structure at 4.0 A resolution of vaccine-elicited antibody A12V163-a.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- 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.1: 7 residues within 4Å: Chain C: T.98, Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 7 residues within 4Å: Chain C: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4, NAG.44 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 6 residues within 4Å: Chain C: N.107 Chain E: N.58, F.114, T.115 Chain F: D.89, T.94 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.58, E:T.115 NAG-NAG-BMA.7: 4 residues within 4Å: Chain C: T.102, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 10 residues within 4Å: Chain C: T.267, H.299, N.301, S.381, T.383 Chain E: R.103, I.104, Y.105, G.106, V.108 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.104 Hydrophobic interactions: E:V.108 NAG-NAG-BMA.13: 4 residues within 4Å: Chain C: N.204, T.206, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 7 residues within 4Å: Chain A: N.56, T.59, R.60 Chain C: E.57, N.58 Chain D: S.17, D.113 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 7 residues within 4Å: Chain K: T.98, Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 7 residues within 4Å: Chain K: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.18, NAG-NAG-BMA-MAN-MAN.18, NAG.47 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 6 residues within 4Å: Chain K: N.107 Chain M: N.58, F.114, T.115 Chain N: D.89, T.94 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:N.58, M:T.115 NAG-NAG-BMA.21: 4 residues within 4Å: Chain K: T.102, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 10 residues within 4Å: Chain K: T.267, H.299, N.301, S.381, T.383 Chain M: R.103, I.104, Y.105, G.106, V.108 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:I.104 Hydrophobic interactions: M:V.108 NAG-NAG-BMA.27: 4 residues within 4Å: Chain K: N.204, T.206, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 7 residues within 4Å: Chain I: N.56, T.59, R.60 Chain K: E.57, N.58 Chain L: S.17, D.113 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 7 residues within 4Å: Chain Q: T.98, Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 7 residues within 4Å: Chain Q: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.32, NAG-NAG-BMA-MAN-MAN.32, NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 6 residues within 4Å: Chain Q: N.107 Chain U: N.58, F.114, T.115 Chain V: D.89, T.94 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:N.58, U:T.115 NAG-NAG-BMA.35: 4 residues within 4Å: Chain Q: T.102, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 10 residues within 4Å: Chain Q: T.267, H.299, N.301, S.381, T.383 Chain U: R.103, I.104, Y.105, G.106, V.108 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:I.104 Hydrophobic interactions: U:V.108 NAG-NAG-BMA.41: 4 residues within 4Å: Chain Q: N.204, T.206, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 7 residues within 4Å: Chain Q: E.57, N.58 Chain R: S.17, D.113 Chain S: N.56, T.59, R.60 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.2: 4 residues within 4Å: Chain C: Q.263, N.265, S.303, R.412 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.263 NAG-NAG-BMA-MAN.12: 4 residues within 4Å: Chain C: N.246 Chain G: Y.111 Chain H: G.29, S.51 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.51 NAG-NAG-BMA-MAN.16: 4 residues within 4Å: Chain K: Q.263, N.265, S.303, R.412 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Q.263 NAG-NAG-BMA-MAN.26: 4 residues within 4Å: Chain K: N.246 Chain O: Y.111 Chain P: G.29, S.51 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:S.51 NAG-NAG-BMA-MAN.30: 4 residues within 4Å: Chain Q: Q.263, N.265, S.303, R.412 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:Q.263 NAG-NAG-BMA-MAN.40: 4 residues within 4Å: Chain Q: N.246 Chain W: Y.111 Chain X: G.29, S.51 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:S.51

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: 6 residues within 4Å: Chain C: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3, NAG.44 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.111 NAG-NAG-BMA-MAN-MAN.11: 6 residues within 4Å: Chain C: E.181, L.231, N.232, V.414, S.415 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.18: 6 residues within 4Å: Chain K: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.17, NAG-NAG-BMA.17, NAG.47 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.111 NAG-NAG-BMA-MAN-MAN.25: 6 residues within 4Å: Chain K: E.181, L.231, N.232, V.414, S.415 Ligands: NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.32: 6 residues within 4Å: Chain Q: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.31, NAG-NAG-BMA.31, NAG.50 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:D.111 NAG-NAG-BMA-MAN-MAN.39: 6 residues within 4Å: Chain Q: E.181, L.231, N.232, V.414, S.415 Ligands: NAG-NAG.38 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.5: 6 residues within 4Å: Chain C: N.103, I.108, D.110, D.111, M.112, R.113 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.113 Hydrogen bonds: C:D.110 NAG-NAG.8: 2 residues within 4Å: Chain C: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.416 Ligands: NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain K: N.103, I.108, D.110, D.111, M.112, R.113 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:R.113 Hydrogen bonds: K:D.110 NAG-NAG.22: 2 residues within 4Å: Chain K: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain K: N.416 Ligands: NAG-NAG-BMA-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 6 residues within 4Å: Chain Q: N.103, I.108, D.110, D.111, M.112, R.113 2 PLIP interactions: 2 interactions with chain Q Hydrophobic interactions: Q:R.113 Hydrogen bonds: Q:D.110 NAG-NAG.36: 2 residues within 4Å: Chain Q: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 2 residues within 4Å: Chain Q: N.416 Ligands: NAG-NAG-BMA-MAN-MAN.39 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 C: N.308 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.308 NAG.44: 3 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG.45: 3 residues within 4Å: Chain C: R.162, N.167 Chain K: R.278 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain K Hydrogen bonds: C:R.162, C:N.167, K:R.278, K:R.278 NAG.46: 1 residues within 4Å: Chain K: N.308 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.308 NAG.47: 3 residues within 4Å: Chain K: N.361 Ligands: NAG-NAG-BMA.17, NAG-NAG-BMA-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG.48: 3 residues within 4Å: Chain K: R.162, N.167 Chain Q: R.278 4 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain K Hydrogen bonds: Q:R.278, Q:R.278, K:R.162, K:N.167 NAG.49: 1 residues within 4Å: Chain Q: N.308 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.308 NAG.50: 3 residues within 4Å: Chain Q: N.361 Ligands: NAG-NAG-BMA.31, NAG-NAG-BMA-MAN-MAN.32 No protein-ligand interaction detected (PLIP) NAG.51: 3 residues within 4Å: Chain C: R.278 Chain Q: R.162, N.167 4 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain C Hydrogen bonds: Q:R.162, Q:N.167, C:R.278, C:R.278

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-a.01 Heavy chain: AIS
A12V163-a.01 Light chain: BJT
Envelope glycoprotein gp120: CKQ
Envelope glycoprotein gp41: DLR
PGT122 Heavy chain: EMU
PGT122 Light chain: FNV
VRC03 Heavy chain: GOW
VRC03 Light chain: HPX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

I
1

S
H

B
4

J
2

T
L

C
B

K
A

Q
C

D
F

L
E

R
D

E
Y

M
X

U
M

F
a

N
Z

V
N

G
g

O
f

W
Q

H
i

P
h

X
R

A12V163-a.01 Heavy chain

A12V163-a.01 Light chain

Envelope glycoprotein gp120

Envelope glycoprotein gp41

PGT122 Heavy chain

PGT122 Light chain

VRC03 Heavy chain

VRC03 Light chain

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