SMTL ID : 6n1w.1

Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody DFPH-a.15 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

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

NAG-NAG.1: 4 residues within 4Å: Chain A: N.103, D.110, M.112, K.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.112 NAG-NAG.3: 6 residues within 4Å: Chain A: T.105, N.118, S.120, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.135 NAG-NAG.4: 6 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.204, T.206, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, S.381, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11 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.12: 2 residues within 4Å: Chain A: P.261, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain I: N.103, D.110, M.112, K.117, K.159, Y.161 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:M.112 NAG-NAG.16: 6 residues within 4Å: Chain I: T.105, N.118, S.120, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Y.135 NAG-NAG.17: 6 residues within 4Å: Chain I: 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 I: N.204, T.206, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 7 residues within 4Å: Chain I: Q.263, N.265, V.302, S.303, S.381, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain I: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain I: P.261, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain Q: N.103, D.110, M.112, K.159, Y.161 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:M.112 NAG-NAG.29: 6 residues within 4Å: Chain Q: T.105, N.118, S.120, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:Y.135 NAG-NAG.30: 6 residues within 4Å: Chain Q: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain Q: N.204, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 8 residues within 4Å: Chain Q: Q.263, N.265, N.301, V.302, S.303, S.381, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.37 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain Q: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 3 residues within 4Å: Chain Q: L.235, P.261, N.416 No protein-ligand interaction detected (PLIP)

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.2: 7 residues within 4Å: Chain A: N.107, I.108 Chain U: Y.50, F.114, T.115 Chain V: D.87, T.92 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:T.115, U:D.56, U:D.56 NAG-NAG-BMA-MAN.10: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA.9, NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 10 residues within 4Å: Chain A: N.64, K.67, T.206, E.245, N.246 Chain X: N.30, A.31, D.49, S.51, F.90 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain X Hydrophobic interactions: A:T.206 Hydrogen bonds: A:K.67, X:D.49, X:S.51 NAG-NAG-BMA-MAN.15: 7 residues within 4Å: Chain D: N.58, F.114, T.115 Chain E: D.87, T.92 Chain I: N.107, I.108 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.58, D:T.115 NAG-NAG-BMA-MAN.23: 5 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG-NAG-BMA.22, NAG-NAG-BMA.22, NAG.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 10 residues within 4Å: Chain F: N.30, A.31, D.49, S.51, F.90 Chain I: N.64, K.67, T.206, E.245, N.246 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain F Hydrophobic interactions: I:T.206 Hydrogen bonds: I:K.67, F:D.49, F:S.51 NAG-NAG-BMA-MAN.28: 8 residues within 4Å: Chain M: Y.50, D.56, F.114, T.115 Chain N: D.87, T.92 Chain Q: N.107, I.108 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:T.115, M:D.56, M:D.56 NAG-NAG-BMA-MAN.36: 5 residues within 4Å: Chain Q: N.355, S.357 Ligands: NAG-NAG-BMA.35, NAG-NAG-BMA.35, NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.39: 9 residues within 4Å: Chain P: N.30, A.31, D.49, S.51, F.90 Chain Q: N.64, K.67, E.245, N.246 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain P Hydrogen bonds: Q:K.67, P:D.49, P:S.51

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: 7 residues within 4Å: Chain A: P.182, L.231, N.232, N.346, G.348, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 6 residues within 4Å: Chain I: L.231, N.232, N.346, G.348, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.32: 6 residues within 4Å: Chain Q: L.231, N.232, N.346, G.348, V.414, S.415 No protein-ligand interaction detected (PLIP)

3 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.9: 7 residues within 4Å: Chain A: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN.10, NAG-NAG-BMA-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 7 residues within 4Å: Chain I: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN.23, NAG-NAG-BMA-MAN.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 6 residues within 4Å: Chain Q: N.332, S.333, T.341, S.357 Ligands: NAG-NAG-BMA-MAN.36, NAG-NAG-BMA-MAN.36 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.11: 18 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, S.381, T.383 Chain U: R.103, I.104, G.106, V.108 Chain V: S.22, N.42, N.43, N.44, P.58, G.59, S.60 Ligands: NAG-NAG.7 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain A Hydrophobic interactions: U:V.108 Hydrogen bonds: U:G.106, U:V.108, A:R.296, U:R.103 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24: 18 residues within 4Å: Chain D: R.103, I.104, G.106, V.108 Chain E: S.22, N.42, N.43, N.44, P.58, G.59, S.60 Chain I: T.267, R.296, H.299, N.301, S.381, T.383 Ligands: NAG-NAG.20 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain D Hydrogen bonds: I:R.296, I:R.296, D:G.106, D:V.108, D:R.103 Hydrophobic interactions: D:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.37: 19 residues within 4Å: Chain M: R.103, I.104, G.106, V.108 Chain N: S.22, N.42, N.43, N.44, P.58, G.59, S.60 Chain Q: N.265, T.267, R.296, H.299, N.301, S.381, T.383 Ligands: NAG-NAG.33 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain M Hydrogen bonds: Q:R.296, M:G.106, M:V.108, M:R.103 Hydrophobic interactions: M:V.108

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

NAG.40: 4 residues within 4Å: Chain A: R.162, N.167 Chain I: R.278 Chain W: Q.76 4 PLIP interactions: 1 interactions with chain W, 2 interactions with chain A, 1 interactions with chain I Hydrogen bonds: W:Q.76, A:R.162, A:N.167, I:R.278 NAG.41: 2 residues within 4Å: Chain A: G.323, N.324 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.324 NAG.42: 3 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG-BMA-MAN.10, NAG-NAG-BMA-MAN.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.361 NAG.43: 4 residues within 4Å: Chain G: Q.76 Chain I: R.162, N.167 Chain Q: R.278 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain Q Hydrogen bonds: I:R.162, I:N.167, Q:R.278 NAG.44: 2 residues within 4Å: Chain I: G.323, N.324 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.324 NAG.45: 3 residues within 4Å: Chain I: N.361 Ligands: NAG-NAG-BMA-MAN.23, NAG-NAG-BMA-MAN.23 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.361 NAG.46: 4 residues within 4Å: Chain A: R.278 Chain O: Q.76 Chain Q: R.162, N.167 5 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain A, 2 interactions with chain O Hydrogen bonds: Q:R.162, Q:N.167, A:R.278, O:Q.76 Hydrophobic interactions: O:Q.76 NAG.47: 2 residues within 4Å: Chain Q: G.323, N.324 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.324 NAG.48: 3 residues within 4Å: Chain Q: N.361 Ligands: NAG-NAG-BMA-MAN.36, NAG-NAG-BMA-MAN.36 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.361

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: AIQ
DFPH-a.15 heavy chain: BKS
DFPH-a.15 Light chain: CLT
PGT122 Heavy chain: DMU
PGT122 Light chain: ENV
VRC03 Light chain: FPX
VRC03 Heavy chain: GOW
Envelope glycoprotein gp41: HJR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

I
C

Q
c

B
3

K
H

S
h

C
4

L
L

T
l

D
5

M
M

U
m

E
6

N
N

V
n

F
7

P
R

X
r

G
8

O
Q

W
q

H
A

J
D

R
d

Envelope glycoprotein gp120

DFPH-a.15 heavy chain

DFPH-a.15 Light chain

PGT122 Heavy chain

PGT122 Light chain

VRC03 Light chain

VRC03 Heavy chain

Envelope glycoprotein gp41

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