SMTL ID : 6cuf.1

Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody vFP1.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.20 Å

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: 8 residues within 4Å: Chain G: N.107 Chain K: G.55, N.58, F.114, T.115 Chain L: W.86, D.87, T.92 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.58, K:T.115 NAG-NAG-BMA-MAN.2: 6 residues within 4Å: Chain G: V.104, T.105, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.135 NAG-NAG-BMA-MAN.14: 8 residues within 4Å: Chain G: N.64, K.67, T.206, N.246 Chain N: A.31, D.49, S.51, F.90 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain G Hydrogen bonds: N:S.51, N:D.49, G:K.67 Hydrophobic interactions: G:T.206 NAG-NAG-BMA-MAN.15: 8 residues within 4Å: Chain C: G.55, N.58, F.114, T.115 Chain D: W.86, D.87, T.92 Chain U: N.107 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.58, C:T.115 NAG-NAG-BMA-MAN.16: 6 residues within 4Å: Chain U: V.104, T.105, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain U Hydrophobic interactions: U:Y.135 NAG-NAG-BMA-MAN.28: 8 residues within 4Å: Chain E: A.31, D.49, S.51, F.90 Chain U: N.64, K.67, T.206, N.246 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain U Hydrogen bonds: E:S.51, U:K.67, E:D.49 Hydrophobic interactions: U:T.206 NAG-NAG-BMA-MAN.29: 8 residues within 4Å: Chain Q: G.55, N.58, F.114, T.115 Chain R: W.86, D.87, T.92 Chain X: N.107 3 PLIP interactions: 3 interactions with chain Q Hydrogen bonds: Q:Y.50, Q:N.58, Q:T.115 NAG-NAG-BMA-MAN.30: 6 residues within 4Å: Chain X: V.104, T.105, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain X Hydrophobic interactions: X:Y.135 NAG-NAG-BMA-MAN.42: 8 residues within 4Å: Chain T: A.31, D.49, S.51, F.90 Chain X: N.64, K.67, T.206, N.246 3 PLIP interactions: 1 interactions with chain T, 2 interactions with chain X Hydrogen bonds: T:S.51, X:K.67, T:D.49 Hydrophobic interactions: X:T.206

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 G: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain G: N.204, T.206, E.245, N.246, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain G: N.332, S.333, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 6 residues within 4Å: Chain U: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 5 residues within 4Å: Chain U: N.204, T.206, E.245, N.246, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 5 residues within 4Å: Chain U: N.332, S.333, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 6 residues within 4Å: Chain X: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 5 residues within 4Å: Chain X: N.204, T.206, E.245, N.246, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 5 residues within 4Å: Chain X: N.332, S.333, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.38, NAG-NAG-BMA-MAN-MAN.38 No protein-ligand interaction detected (PLIP)

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.4: 6 residues within 4Å: Chain G: R.162, I.164, N.167, T.168 Chain M: Q.76 Chain X: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain G: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain G: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain G: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain G: P.261, V.414, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain F: Q.76 Chain G: R.278 Chain U: R.162, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain U: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain U: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain U: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain U: P.261, V.414, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 6 residues within 4Å: Chain S: Q.76 Chain U: R.278 Chain X: R.162, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain X: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain X: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 5 residues within 4Å: Chain X: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.38, NAG-NAG-BMA-MAN-MAN.38, NAG-NAG-BMA-MAN-MAN.38 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain X: P.261, V.414, N.416 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.6: 8 residues within 4Å: Chain G: S.179, L.231, 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.20: 8 residues within 4Å: Chain U: S.179, L.231, N.232, R.274, N.346, G.348, V.414, S.415 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:G.348 NAG-NAG-BMA-MAN-MAN-MAN.34: 8 residues within 4Å: Chain X: S.179, L.231, N.232, R.274, N.346, G.348, V.414, S.415 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:G.348

3 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.10: 6 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA.9, NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.24: 6 residues within 4Å: Chain U: N.355, S.357 Ligands: NAG-NAG-BMA.23, NAG-NAG-BMA.23, NAG-NAG.25, NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.38: 6 residues within 4Å: Chain X: N.355, S.357 Ligands: NAG-NAG-BMA.37, NAG-NAG-BMA.37, NAG-NAG.39, NAG-NAG.39 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.12: 17 residues within 4Å: Chain G: N.265, T.267, R.296, H.299, N.301, S.381, T.383 Chain K: R.103, I.104, G.106 Chain L: S.22, N.42, N.43, N.44, P.58, G.59, S.60 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.296, G:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.26: 18 residues within 4Å: Chain C: R.103, I.104, G.106, V.107 Chain D: S.22, N.42, N.43, N.44, P.58, G.59, S.60 Chain U: N.265, T.267, R.296, H.299, N.301, S.381, T.383 3 PLIP interactions: 2 interactions with chain U, 1 interactions with chain C Hydrogen bonds: U:R.296, U:R.296, C:G.106 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.40: 16 residues within 4Å: Chain Q: R.103, I.104, G.106 Chain R: N.42, N.43, N.44, P.58, G.59, S.60 Chain X: N.265, T.267, R.296, H.299, N.301, S.381, T.383 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain Q Hydrogen bonds: X:R.296, X:R.296, Q:G.106

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

NAG.43: 3 residues within 4Å: Chain G: N.103, I.108, R.140 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.140, G:R.140 NAG.44: 2 residues within 4Å: Chain G: K.316, N.324 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.316 NAG.45: 1 residues within 4Å: Chain H: N.126 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.126 NAG.46: 3 residues within 4Å: Chain U: N.103, I.108, R.140 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:R.140, U:R.140 NAG.47: 2 residues within 4Å: Chain U: K.316, N.324 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:K.316 NAG.48: 1 residues within 4Å: Chain V: N.126 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:N.126 NAG.49: 1 residues within 4Å: Chain W: N.126 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:N.126 NAG.50: 3 residues within 4Å: Chain X: N.103, I.108, R.140 2 PLIP interactions: 2 interactions with chain X Hydrogen bonds: X:R.140, X:R.140 NAG.51: 2 residues within 4Å: Chain X: K.316, N.324 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:K.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dingens, A.S. et al., Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV. PLoS Pathog. (2018)

Release Date

2018-07-25

Peptides

vFP1.01 heavy chain: AIO
vFP1.01 Light chain: BJP
PGT122 Heavy chain: CKQ
PGT122 light chain: DLR
VRC03 light chain: ENT
VRC03 heavy chain: FMS
Envelope glycoprotein gp120: GUX
Envelope glycoprotein gp41: HVW

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

I
H

O
h

B
4

J
L

P
l

C
5

K
M

Q
m

D
6

L
N

R
n

E
7

N
R

T
r

F
8

M
Q

S
q

G
C

U
2

X
d

H
D

V
A

W
c

vFP1.01 heavy chain

vFP1.01 Light chain

PGT122 Heavy chain

PGT122 light chain

VRC03 light chain

VRC03 heavy chain

Envelope glycoprotein gp120

Envelope glycoprotein gp41

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