SMTL ID : 6cue.1

Cryo-EM structure at 4.0 A resolution of vaccine-elicited antibody vFP7.04 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.00 Å

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: N.103, D.110, R.113, R.140 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: Q.100, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.204, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain A: P.261, V.414, N.416 Chain T: R.24, D.75 Ligands: NAG-NAG-BMA-MAN-MAN.6 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:R.24, T:R.24 NAG-NAG.14: 3 residues within 4Å: Chain B: N.103, D.110, R.113 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain B: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain B: N.204, T.206, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain B: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain B: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain B: N.355, S.357 Ligands: NAG-NAG-BMA.22 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain B: P.261, V.414, N.416 Chain F: R.24, D.75 Ligands: NAG-NAG-BMA-MAN-MAN.19 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.24, F:R.24, F:D.75 NAG-NAG.27: 4 residues within 4Å: Chain C: N.103, T.109, D.110, R.140 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain C: Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 5 residues within 4Å: Chain C: N.204, T.206, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain C: Q.263, N.265, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain C: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG-BMA.35 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 6 residues within 4Å: Chain C: P.261, V.414, N.416 Chain M: R.24, D.75 Ligands: NAG-NAG-BMA-MAN-MAN.32 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:R.24

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.2: 8 residues within 4Å: Chain A: N.107, T.109 Chain U: N.58, T.115 Chain V: D.89, R.92, P.93, T.94 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:N.58, U:T.115 NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: T.105, N.118, Y.135, D.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.135 NAG-NAG-BMA.9: 5 residues within 4Å: Chain A: N.332, S.333, S.357 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 8 residues within 4Å: Chain B: N.107, T.109 Chain G: N.58, T.115 Chain H: D.89, R.92, P.93, T.94 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.58, G:T.115 NAG-NAG-BMA.16: 4 residues within 4Å: Chain B: T.105, N.118, Y.135, D.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.135 NAG-NAG-BMA.22: 5 residues within 4Å: Chain B: N.332, S.333, S.357 Ligands: NAG-NAG.23, NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 6 residues within 4Å: Chain C: N.107, T.109 Chain N: N.58, T.115 Chain O: P.93, T.94 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:N.58, N:T.115 NAG-NAG-BMA.29: 4 residues within 4Å: Chain C: T.105, N.118, Y.135, D.290 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.135 NAG-NAG-BMA.35: 4 residues within 4Å: Chain C: N.332, S.333 Ligands: NAG-NAG.36, NAG-NAG.36 No protein-ligand interaction detected (PLIP)

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.6: 8 residues within 4Å: Chain A: P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN.19: 7 residues within 4Å: Chain B: L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.32: 9 residues within 4Å: Chain C: E.181, P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.38 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.11: 15 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, S.381 Chain U: R.103, I.104, G.106, V.107 Chain V: S.24, N.44, N.45, P.60, G.61, S.62 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain V Hydrogen bonds: A:R.296, V:N.44, V:N.44, V:N.45, V:G.61 NAG-NAG-BMA-MAN-MAN.24: 16 residues within 4Å: Chain B: T.267, R.296, H.299, N.301, S.381, T.383 Chain G: R.103, I.104, G.106, V.107 Chain H: S.24, N.44, N.45, P.60, G.61, S.62 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain H Hydrogen bonds: B:R.296, H:N.44, H:N.44, H:N.45, H:G.61 NAG-NAG-BMA-MAN-MAN.37: 15 residues within 4Å: Chain C: T.267, H.299, N.301, S.381, T.383 Chain N: R.103, I.104, G.106, V.107 Chain O: S.24, N.44, N.45, P.60, G.61, S.62 4 PLIP interactions: 4 interactions with chain O Hydrogen bonds: O:N.44, O:N.44, O:N.45, O:G.61

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.13: 7 residues within 4Å: Chain A: K.67, E.245, N.246 Chain W: Y.111 Chain X: A.31, S.51, F.90 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain W, 1 interactions with chain X Hydrogen bonds: A:K.67, W:Y.111, X:S.51 NAG-NAG-BMA-MAN.26: 7 residues within 4Å: Chain B: N.64, K.67, E.245, N.246 Chain I: Y.111 Chain J: S.51, F.90 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain J Hydrogen bonds: B:N.64, B:K.67, J:S.51, J:S.51 NAG-NAG-BMA-MAN.39: 6 residues within 4Å: Chain C: K.67, E.245, N.246 Chain P: Y.111 Chain Q: S.51, F.90 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain Q Hydrogen bonds: C:K.67, Q:S.51, Q:S.51

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

NAG.40: 3 residues within 4Å: Chain A: R.162, N.167 Chain C: R.278 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.162, A:N.167, C:R.278 NAG.41: 2 residues within 4Å: Chain B: R.162, N.167 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.162, B:N.167, A:R.278 NAG.42: 3 residues within 4Å: Chain C: R.162, N.167 Chain P: Q.76 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.162, C:N.167

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

2018-07-11

Peptides

Envelope glycoprotein gp120: ABC
Envelope glycoprotein gp41: DKR
vFP7.04 Heavy chain: ELS
vFP7.04 light chain: FMT
PGT122 heavy Chain: GNU
PGT122 Light chain: HOV
VRC03 Heavy chain: IPW
VRC03 light chain: JQX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
c

B
2

C
C

D
1

K
D

R
d

E
3

L
H

S
h

F
4

M
L

T
l

G
5

N
M

U
m

H
6

O
N

V
n

I
7

P
Q

W
q

J
8

Q
R

X
r

Envelope glycoprotein gp120

Envelope glycoprotein gp41

vFP7.04 Heavy chain

vFP7.04 light chain

PGT122 heavy Chain

PGT122 Light chain

VRC03 Heavy chain

VRC03 light chain

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