SMTL ID : 5uty.1

Crystal Structure of a Stabilized DS-SOSIP.mut4 BG505 gp140 HIV-1 Env Trimer, Containing Mutations I201C-P433C (DS), L154M, N300M, N302M, T320L in Complex with Human Antibodies PGT122 and 35O22 at 4.1 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.1: 19 residues within 4Å: Chain A: L.9, S.17 Chain B: R.28, N.30, F.31, H.33, W.50, S.52, Y.54, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain C: H.95, N.96 Chain D: N.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.115, B:D.111, B:G.112, B:H.33, B:S.52, B:S.52, B:D.111 NAG-NAG-BMA-MAN-MAN-MAN.23: 19 residues within 4Å: Chain G: L.9, S.17 Chain H: R.28, N.30, F.31, H.33, W.50, S.52, Y.54, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain I: H.95, N.96 Chain J: N.82 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:T.115, H:D.111, H:G.112, H:H.33, H:S.52, H:S.52, H:D.111 NAG-NAG-BMA-MAN-MAN-MAN.45: 19 residues within 4Å: Chain M: L.9, S.17 Chain N: R.28, N.30, F.31, H.33, W.50, S.52, Y.54, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain O: H.95, N.96 Chain P: N.82 4 PLIP interactions: 4 interactions with chain N Hydrogen bonds: N:T.115, N:D.111, N:G.112, N:H.33, N:S.52, N:S.52, N:D.111

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.2: 7 residues within 4Å: Chain D: N.131 Chain E: N.58, R.102, F.114, T.115 Chain F: D.87, T.92 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.102, E:N.58, E:T.115, E:T.115 NAG-NAG-BMA-MAN.24: 7 residues within 4Å: Chain J: N.131 Chain K: N.58, R.102, F.114, T.115 Chain L: D.87, T.92 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:R.102, K:N.58, K:T.115, K:T.115 NAG-NAG-BMA-MAN.46: 7 residues within 4Å: Chain P: N.131 Chain Q: N.58, R.102, F.114, T.115 Chain R: D.87, T.92 3 PLIP interactions: 3 interactions with chain Q Hydrogen bonds: Q:R.102, Q:N.58, Q:T.115, Q:T.115

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.3: 4 residues within 4Å: Chain D: T.129, N.142, S.144, Y.159 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.25: 4 residues within 4Å: Chain J: T.129, N.142, S.144, Y.159 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.47: 4 residues within 4Å: Chain P: T.129, N.142, S.144, Y.159 No protein-ligand interaction detected (PLIP)

27 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: 5 residues within 4Å: Chain D: T.122, Q.124, N.146, K.155, K.157 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain D: V.168, R.186, N.191 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: P.77, V.78 Chain D: N.228, T.230, S.268 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: Q.287, N.289, N.325, S.327 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: N.295, I.316, V.434 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain D: N.356, S.357, N.379, S.381 Ligands: NAG-NAG.12, NAG-NAG.12, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain D: N.379, S.381 Ligands: NAG-NAG.11, NAG-NAG.11, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain D: N.385 Ligands: NAG-NAG.11, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain D: N.256, P.285, N.440 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain J: T.122, Q.124, N.146, K.155, K.157 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain J: V.168, R.186, N.191 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain H: P.77, V.78 Chain J: N.228, T.230, S.268 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain J: Q.287, N.289, N.325, S.327 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain J: N.295, I.316, V.434 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 7 residues within 4Å: Chain J: N.356, S.357, N.379, S.381 Ligands: NAG-NAG.34, NAG-NAG.34, NAG-NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain J: N.379, S.381 Ligands: NAG-NAG.33, NAG-NAG.33, NAG-NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain J: N.385 Ligands: NAG-NAG.33, NAG-NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 4 residues within 4Å: Chain J: N.256, P.285, N.440 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.29 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 5 residues within 4Å: Chain P: T.122, Q.124, N.146, K.155, K.157 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 3 residues within 4Å: Chain P: V.168, R.186, N.191 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 5 residues within 4Å: Chain N: P.77, V.78 Chain P: N.228, T.230, S.268 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 4 residues within 4Å: Chain P: Q.287, N.289, N.325, S.327 No protein-ligand interaction detected (PLIP) NAG-NAG.53: 3 residues within 4Å: Chain P: N.295, I.316, V.434 No protein-ligand interaction detected (PLIP) NAG-NAG.55: 7 residues within 4Å: Chain P: N.356, S.357, N.379, S.381 Ligands: NAG-NAG.56, NAG-NAG.56, NAG-NAG.57 No protein-ligand interaction detected (PLIP) NAG-NAG.56: 5 residues within 4Å: Chain P: N.379, S.381 Ligands: NAG-NAG.55, NAG-NAG.55, NAG-NAG.57 No protein-ligand interaction detected (PLIP) NAG-NAG.57: 3 residues within 4Å: Chain P: N.385 Ligands: NAG-NAG.55, NAG-NAG.56 No protein-ligand interaction detected (PLIP) NAG-NAG.58: 4 residues within 4Å: Chain P: N.256, P.285, N.440 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.51 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.7: 9 residues within 4Å: Chain D: K.59, E.205, P.206, N.256, N.370, G.372, V.438, S.439 Ligands: NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.29: 9 residues within 4Å: Chain J: K.59, E.205, P.206, N.256, N.370, G.372, V.438, S.439 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.51: 9 residues within 4Å: Chain P: K.59, E.205, P.206, N.256, N.370, G.372, V.438, S.439 Ligands: NAG-NAG.58 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-MAN.10: 15 residues within 4Å: Chain D: T.291, R.320, H.323, N.325, T.407 Chain E: R.103, I.104, G.106, V.107 Chain F: S.22, N.42, N.43, P.58, G.59, S.60 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.320, E:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.32: 15 residues within 4Å: Chain J: T.291, R.320, H.323, N.325, T.407 Chain K: R.103, I.104, G.106, V.107 Chain L: S.22, N.42, N.43, P.58, G.59, S.60 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:V.107, J:R.320 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.54: 15 residues within 4Å: Chain P: T.291, R.320, H.323, N.325, T.407 Chain Q: R.103, I.104, G.106, V.107 Chain R: S.22, N.42, N.43, P.58, G.59, S.60 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain P Hydrogen bonds: Q:V.107, P:R.320

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

NAG.15: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.107 Chain C: N.54, E.55, R.56 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: E.123, N.126 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: N.127, R.137 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: N.270, T.272, N.273 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain D: K.344, N.348 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: N.332, W.388 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain E: N.23, V.24, K.75, L.77 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain G: N.107 Chain I: N.54, E.55, R.56 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: E.123, N.126 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain J: N.127, R.137 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain J: N.270, T.272, N.273 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain J: K.344, N.348 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain J: N.332, W.388 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain K: N.23, V.24, K.75, L.77 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain M: N.100, S.102 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain M: N.107 Chain O: N.54, E.55, R.56 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain M: E.123, N.126 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain P: N.127, R.137 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain P: N.270, T.272, N.273 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain P: K.344, N.348 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain P: N.332, W.388 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain Q: N.23, V.24, K.75, L.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuang, G.Y. et al., Structure-Based Design of a Soluble Prefusion-Closed HIV-1 Env Trimer with Reduced CD4 Affinity and Improved Immunogenicity. J. Virol. (2017)

Release Date

2017-03-29

Peptides

HIV-1 BG505 strain Env gp41: AGM
35O22 Fab heavy chain: BHN
35O22 Fab light chain: CIO
HIV-1 BG505 strain Env gp120: DJP
PGT122 Fab heavy chain: EKQ
PGT122 Fab 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

HIV-1 BG505 strain Env gp41

35O22 Fab heavy chain

35O22 Fab light chain

HIV-1 BG505 strain Env gp120

PGT122 Fab heavy chain

PGT122 Fab light chain

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