SMTL ID : 6vpx.1

Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 5.00 Å

Oligo State

hetero-3-3-3-3-3-1-1-mer

Ligands

12 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: 1 residues within 4Å: Chain A: N.100 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.240, T.242, D.243 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: M.335, N.348, T.350 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: E.257, N.259, S.297 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.265, I.286 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain A: L.104, N.120, S.122, K.135, Y.137, E.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.135 NAG-NAG.10: 3 residues within 4Å: Chain A: E.232, N.253, Q.307 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: E.53, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: E.57, N.58 Chain D: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: T.98, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain C: V.55, N.193, D.194, T.204, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: N.348, T.350, Q.351 Ligands: NAG.59 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.193, K.195, N.205 No protein-ligand interaction detected (PLIP)

1 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.6: 8 residues within 4Å: Chain A: P.176, L.225, N.226, N.339, R.402, S.404, S.405 Ligands: NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP)

2 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.8: 7 residues within 4Å: Chain A: N.226, L.229, S.255, S.404, S.405, N.406 Ligands: NAG-NAG-BMA-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 8 residues within 4Å: Chain B: V.218, L.225, N.226, N.339, G.341, C.403, S.404, S.405 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.341

1 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.16: 8 residues within 4Å: Chain C: E.34, N.226, N.339, I.397, C.403, S.404, S.405 Ligands: NAG.51 No protein-ligand interaction detected (PLIP)

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.17: 4 residues within 4Å: Chain C: V.146, I.148, R.156, N.161 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.149, C:R.156 NAG-FUC.23: 1 residues within 4Å: Chain E: N.114 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.19: 2 residues within 4Å: Chain D: E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.20: 3 residues within 4Å: Chain D: N.100, S.102, Y.127 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.127

1 x NAG- NAG- BMA- MAN- NAG- GAL- NAG- MAN- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-NAG-MAN-FUC.21: 17 residues within 4Å: Chain E: R.122, E.123, N.126 Chain P: V.1, D.25, F.26, P.27, K.30, Y.31, R.97, F.99, Q.100, E.101, S.102 Chain Q: N.32, F.59, S.60 5 PLIP interactions: 4 interactions with chain P, 1 interactions with chain Q Hydrogen bonds: P:V.1, P:V.1, P:D.25, P:F.26, P:R.97, P:Y.31, P:E.101, P:E.101, P:E.101, Q:N.32

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-MAN-FUC.22: 14 residues within 4Å: Chain E: N.100, S.102, Y.127, L.130 Chain P: R.18, D.53, A.54, W.55, L.68, S.70, R.71, Y.79, E.81, P.105 6 PLIP interactions: 5 interactions with chain P, 1 interactions with chain E Hydrophobic interactions: P:P.105, E:Y.127 Hydrogen bonds: P:R.18, P:S.70, P:R.71, P:R.71, P:E.81

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

NAG.24: 2 residues within 4Å: Chain A: N.124, V.133 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: R.156, N.161 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.198, T.200, S.238 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: N.259, T.261, H.293, N.295, V.373 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.354 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: E.57, N.58 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.152, T.153 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: G.317, N.318 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.324, R.427 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.124, Q.134, K.135 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: L.104, N.120, L.139 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.240, T.242, D.243 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: E.232, E.233, N.253, K.254, Q.307 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain B: T.261, H.293, N.295, T.371, V.373, R.402 Ligand excluded by PLIP NAG.38: 7 residues within 4Å: Chain B: E.257, N.259, N.295, I.296, S.297, T.371, R.402 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.265, Q.400 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: Q.351, N.354 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.324 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain B: N.198, T.200, S.238, A.239, F.241 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: N.318, K.319 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.152 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: R.156, N.161, T.162 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.100 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: L.229, S.255, N.406 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain B: E.57, N.58 Chain F: G.16, S.17 Chain M: G.8, G.9 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.100, N.152 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.198, T.200 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: S.255, N.406 Ligands: NAG-NAG-BMA-MAN-MAN.16 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.240, T.242, D.243 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.120, Y.137 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.152 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain C: N.259, N.295, I.296, S.297, R.402 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.265, I.286 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain C: H.293, N.295, T.371, V.373, R.402 Ligand excluded by PLIP NAG.58: 6 residues within 4Å: Chain C: E.232, V.234, N.253, K.254, Q.307, K.311 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain C: Q.351, N.354 Ligands: NAG-NAG.18 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain C: N.318, K.319 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain C: N.324, H.325, I.425, R.427 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain D: N.114 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain F: N.105, K.106, Q.110 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain F: N.114 Chain M: V.5 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain F: N.126 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain F: N.100, S.102, L.130 Ligand excluded by PLIP

3 x 44E: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate(Non-covalent)

44E.67: 4 residues within 4Å: Chain G: S.109 Chain H: L.26, R.27, Y.30 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Y.30, H:Y.30 44E.68: 4 residues within 4Å: Chain J: S.109 Chain K: L.26, R.27, Y.30 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.30 44E.69: 4 residues within 4Å: Chain M: S.109 Chain N: L.26, R.27, Y.30 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:Y.30, N:Y.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rantalainen, K. et al., HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies. Cell Rep (2020)

Release Date

2020-04-22

Peptides

Envelope glycoprotein gp120: ABC
Envelope glycoprotein gp41: DEF
Antibody 10E8 Fab heavy chain: GJM
Antibody 10E8 Fab light chain: HKN
MPER peptide: ILO
Antibody PGT151 Fab heavy chain: P
Antibody PGT151 Fab light chain: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
C

D
D

E
B

F
F

G
H

J
K

M
M

H
L

K
N

N
O

I
G

L
I

O
J

P
P

Q
Q

Envelope glycoprotein gp120

Envelope glycoprotein gp41

Antibody 10E8 Fab heavy chain

Antibody 10E8 Fab light chain

MPER peptide

Antibody PGT151 Fab heavy chain

Antibody PGT151 Fab light chain