SMTL ID : 6de7.1

Crystal Structure at 4.3 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Interdomain Stabilization 113C-429GCG in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.12 Å

Oligo State

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

Ligands

6 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: 3 residues within 4Å: Chain A: K.122, E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain D: N.232, L.235, P.261, N.418 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 3 residues within 4Å: Chain G: K.122, E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 5 residues within 4Å: Chain J: N.232, L.235, P.261, N.418 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.45: 3 residues within 4Å: Chain M: K.122, E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.53: 5 residues within 4Å: Chain P: N.232, L.235, P.261, N.418 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.49 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(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)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.2: 13 residues within 4Å: Chain A: S.17 Chain B: N.30, F.31, Y.32, H.33, D.57, R.110, G.112, S.113, T.115 Chain C: H.95, N.96 Chain D: N.58 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.115, B:T.115, B:H.33, B:T.115, C:H.95 Hydrophobic interactions: B:R.110 NAG-NAG-BMA-MAN-MAN-MAN-MAN.24: 13 residues within 4Å: Chain G: S.17 Chain H: N.30, F.31, Y.32, H.33, D.57, R.110, G.112, S.113, T.115 Chain I: H.95, N.96 Chain J: N.58 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:T.115, H:T.115, H:H.33, H:T.115, I:H.95 Hydrophobic interactions: H:R.110 NAG-NAG-BMA-MAN-MAN-MAN-MAN.46: 13 residues within 4Å: Chain M: S.17 Chain N: N.30, F.31, Y.32, H.33, D.57, R.110, G.112, S.113, T.115 Chain O: H.95, N.96 Chain P: N.58 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain O Hydrogen bonds: N:T.115, N:T.115, N:H.33, N:T.115, O:H.95 Hydrophobic interactions: N:R.110

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.3: 9 residues within 4Å: Chain D: N.107 Chain E: R.102, W.113, T.115 Chain F: D.89, S.90, R.92, P.93, T.94 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.115, E:R.102 NAG-NAG-BMA-MAN.25: 9 residues within 4Å: Chain J: N.107 Chain K: R.102, W.113, T.115 Chain L: D.89, S.90, R.92, P.93, T.94 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:T.115, K:R.102 NAG-NAG-BMA-MAN.47: 9 residues within 4Å: Chain P: N.107 Chain Q: R.102, W.113, T.115 Chain R: D.89, S.90, R.92, P.93, T.94 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:T.115, Q:R.102

24 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: 4 residues within 4Å: Chain D: W.66, N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain D: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.7, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: R.329, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain D: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain D: N.265, N.301, V.302, S.303, S.381, R.414, V.416 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain D: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain J: W.66, N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 6 residues within 4Å: Chain J: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.29, NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain J: N.355, S.357 Ligands: NAG-NAG.28, NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain J: R.329, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain J: N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain J: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 7 residues within 4Å: Chain J: N.265, N.301, V.302, S.303, S.381, R.414, V.416 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain J: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 4 residues within 4Å: Chain P: W.66, N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 6 residues within 4Å: Chain P: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.51, NAG-NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.51: 4 residues within 4Å: Chain P: N.355, S.357 Ligands: NAG-NAG.50, NAG-NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 2 residues within 4Å: Chain P: R.329, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.55: 3 residues within 4Å: Chain P: N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.56: 3 residues within 4Å: Chain P: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.57: 7 residues within 4Å: Chain P: N.265, N.301, V.302, S.303, S.381, R.414, V.416 No protein-ligand interaction detected (PLIP) NAG-NAG.58: 2 residues within 4Å: Chain P: N.271, I.292 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.5: 11 residues within 4Å: Chain D: K.35, N.37, S.179, E.181, P.182, N.232, N.346, R.414, V.416, S.417 Ligands: NAG-NAG-BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.27: 11 residues within 4Å: Chain J: K.35, N.37, S.179, E.181, P.182, N.232, N.346, R.414, V.416, S.417 Ligands: NAG-NAG-BMA.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.49: 11 residues within 4Å: Chain P: K.35, N.37, S.179, E.181, P.182, N.232, N.346, R.414, V.416, S.417 Ligands: NAG-NAG-BMA.53 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.10: 3 residues within 4Å: Chain D: T.105, N.118 Chain F: R.91 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.32: 3 residues within 4Å: Chain J: T.105, N.118 Chain L: R.91 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.54: 3 residues within 4Å: Chain P: T.105, N.118 Chain R: R.91 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.15: 15 residues within 4Å: Chain D: T.267, H.299, N.301, T.383 Chain E: R.103, I.104, G.106, V.107 Chain F: S.24, N.44, N.45, N.46, P.60, G.61, S.62 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.37: 15 residues within 4Å: Chain J: T.267, H.299, N.301, T.383 Chain K: R.103, I.104, G.106, V.107 Chain L: S.24, N.44, N.45, N.46, P.60, G.61, S.62 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.59: 15 residues within 4Å: Chain P: T.267, H.299, N.301, T.383 Chain Q: R.103, I.104, G.106, V.107 Chain R: S.24, N.44, N.45, N.46, P.60, G.61, S.62 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:V.107

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

NAG.16: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.105, N.107 Chain C: E.55, R.56 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: N.246, T.248 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: N.308, S.362, W.364 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: R.319, K.320, N.324 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: N.103, D.110 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain G: N.105, N.107 Chain I: E.55, R.56 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain J: N.246, T.248 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain J: N.308, S.362, W.364 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain J: R.319, K.320, N.324 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain J: N.103, D.110 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain M: N.100, S.102 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain M: N.105, N.107 Chain O: E.55, R.56 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain P: N.246, T.248 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain P: N.308, S.362, W.364 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain P: R.319, K.320, N.324 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain P: N.103, D.110 Ligand excluded by PLIP

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.22: 5 residues within 4Å: Chain D: R.128 Chain J: R.128 Chain P: R.128 Ligands: SO4.44, SO4.66 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 1 interactions with chain P Salt bridges: J:R.128, D:R.128, P:R.128 SO4.44: 5 residues within 4Å: Chain D: R.128 Chain J: R.128 Chain P: R.128 Ligands: SO4.22, SO4.66 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 1 interactions with chain P Salt bridges: J:R.128, D:R.128, P:R.128 SO4.66: 5 residues within 4Å: Chain D: R.128 Chain J: R.128 Chain P: R.128 Ligands: SO4.22, SO4.44 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 1 interactions with chain P Salt bridges: J:R.128, D:R.128, P:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, P. et al., Interdomain Stabilization Impairs CD4 Binding and Improves Immunogenicity of the HIV-1 Envelope Trimer. Cell Host Microbe (2018)

Release Date

2018-06-06

Peptides

Envelope glycoprotein gp160: AGM
35O22 heavy chain: BHN
35O22 light chain: CIO
Envelope glycoprotein gp160: DJP
PGT122 Heavy chain: EKQ
PGT122 Light Chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

G
B

M
B

B
D

H
D

N
D

C
E

I
E

O
E

D
G

J
G

P
G

E
H

K
H

Q
H

F
L

L
L

R
L

Envelope glycoprotein gp160

35O22 heavy chain

35O22 light chain

Envelope glycoprotein gp160

PGT122 Heavy chain

PGT122 Light Chain

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