SMTL ID : 6ch9.1

Crystal structure of a natively-glycosylated B41 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.85 Å

Oligo State

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

Ligands

21 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: N.105, K.106 Chain B: E.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: D.125, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain D: N.165, C.166, Y.182, A.183 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain D: N.250, G.251, S.252 Ligands: NAG-NAG-BMA-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain D: N.354, G.358, W.409, T.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain D: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain D: A.307, E.309, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain G: N.105, K.106 Chain H: E.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain G: D.125, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 4 residues within 4Å: Chain J: N.165, C.166, Y.182, A.183 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 4 residues within 4Å: Chain J: N.250, G.251, S.252 Ligands: NAG-NAG-BMA-MAN.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 4 residues within 4Å: Chain J: N.354, G.358, W.409, T.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 2 residues within 4Å: Chain J: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 5 residues within 4Å: Chain J: A.307, E.309, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 3 residues within 4Å: Chain M: N.105, K.106 Chain N: E.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 2 residues within 4Å: Chain M: D.125, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 4 residues within 4Å: Chain P: N.165, C.166, Y.182, A.183 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.44: 4 residues within 4Å: Chain P: N.250, G.251, S.252 Ligands: NAG-NAG-BMA-MAN.47 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.49: 4 residues within 4Å: Chain P: N.354, G.358, W.409, T.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.50: 2 residues within 4Å: Chain P: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.52: 5 residues within 4Å: Chain P: A.307, E.309, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.46 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.3: 14 residues within 4Å: Chain A: G.16, S.17, D.113 Chain B: F.31, H.33, W.50, Y.54, S.55, D.57, S.114, T.115, W.116 Chain C: H.95 Chain D: N.93 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.114, A:D.113, B:S.52, B:T.115, B:D.57, B:W.116 NAG-NAG-BMA-MAN.22: 14 residues within 4Å: Chain G: G.16, S.17, D.113 Chain H: F.31, H.33, W.50, Y.54, S.55, D.57, S.114, T.115, W.116 Chain I: H.95 Chain J: N.93 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:S.114, H:S.52, H:T.115, G:D.113, H:D.57, H:W.116 NAG-NAG-BMA-MAN.41: 14 residues within 4Å: Chain M: G.16, S.17, D.113 Chain N: F.31, H.33, W.50, Y.54, S.55, D.57, S.114, T.115, W.116 Chain O: H.95 Chain P: N.93 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:S.114, M:D.113, N:S.52, N:T.115, N:D.57, N:W.116

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

NAG-NAG.5: 6 residues within 4Å: Chain D: T.133, L.134, N.135, S.167, F.168, N.169 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.135 NAG-NAG.7: 7 residues within 4Å: Chain D: E.88, V.90, K.243, C.244, N.245, N.257, S.259 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.88 NAG-NAG.10: 4 residues within 4Å: Chain D: N.317, I.338, R.451, G.452 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain J: T.133, L.134, N.135, S.167, F.168, N.169 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.135 NAG-NAG.26: 7 residues within 4Å: Chain J: E.88, V.90, K.243, C.244, N.245, N.257, S.259 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.88 NAG-NAG.29: 4 residues within 4Å: Chain J: N.317, I.338, R.451, G.452 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 6 residues within 4Å: Chain P: T.133, L.134, N.135, S.167, F.168, N.169 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.135 NAG-NAG.45: 7 residues within 4Å: Chain P: E.88, V.90, K.243, C.244, N.245, N.257, S.259 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:E.88 NAG-NAG.48: 4 residues within 4Å: Chain P: N.317, I.338, R.451, G.452 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: 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.8: 13 residues within 4Å: Chain D: T.68, E.69, E.227, P.228, R.268, L.277, N.278, Q.453, C.456, S.457, S.458, N.459 Ligands: NAG-NAG-BMA.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.457 NAG-NAG-BMA-MAN-MAN-MAN.27: 13 residues within 4Å: Chain J: T.68, E.69, E.227, P.228, R.268, L.277, N.278, Q.453, C.456, S.457, S.458, N.459 Ligands: NAG-NAG-BMA.33 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.457 NAG-NAG-BMA-MAN-MAN-MAN.46: 13 residues within 4Å: Chain P: T.68, E.69, E.227, P.228, R.268, L.277, N.278, Q.453, C.456, S.457, S.458, N.459 Ligands: NAG-NAG-BMA.52 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:S.457

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.9: 5 residues within 4Å: Chain D: N.292, I.293, T.294, D.295 Ligands: NAG-NAG-BMA.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.294 NAG-NAG-BMA-MAN.28: 5 residues within 4Å: Chain J: N.292, I.293, T.294, D.295 Ligands: NAG-NAG-BMA.25 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:T.294 NAG-NAG-BMA-MAN.47: 5 residues within 4Å: Chain P: N.292, I.293, T.294, D.295 Ligands: NAG-NAG-BMA.44 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:T.294

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.13: 7 residues within 4Å: Chain D: N.406 Chain E: N.55, A.57, T.58, T.59 Chain F: S.95, D.96 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.55, E:N.55 NAG-NAG-BMA-MAN-MAN.32: 7 residues within 4Å: Chain J: N.406 Chain K: N.55, A.57, T.58, T.59 Chain L: S.95, D.96 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.55, K:N.55 NAG-NAG-BMA-MAN-MAN.51: 7 residues within 4Å: Chain P: N.406 Chain Q: N.55, A.57, T.58, T.59 Chain R: S.95, D.96 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:N.55, Q:N.55

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-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.15: 16 residues within 4Å: Chain D: R.342, H.345, N.347, G.421, E.422, N.424 Chain E: R.102, I.103, Y.104, G.105, V.106, V.107, E.111, F.113 Chain F: S.52 Ligands: NAG.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.106 NAG-NAG-BMA-MAN-MAN-MAN.34: 16 residues within 4Å: Chain J: R.342, H.345, N.347, G.421, E.422, N.424 Chain K: R.102, I.103, Y.104, G.105, V.106, V.107, E.111, F.113 Chain L: S.52 Ligands: NAG.37 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:V.106 NAG-NAG-BMA-MAN-MAN-MAN.53: 16 residues within 4Å: Chain P: R.342, H.345, N.347, G.421, E.422, N.424 Chain Q: R.102, I.103, Y.104, G.105, V.106, V.107, E.111, F.113 Chain R: S.52 Ligands: NAG.56 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:V.106

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

NAG.16: 5 residues within 4Å: Chain A: E.110, N.114 Chain B: Y.32, Y.119 Chain C: P.58 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:P.58, A:E.110 Hydrogen bonds: B:Y.32, B:Y.32, B:Y.119, B:Y.119 NAG.17: 2 residues within 4Å: Chain D: R.208, N.213 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.208 NAG.18: 4 residues within 4Å: Chain D: N.311, G.421, E.422 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.421 NAG.19: 3 residues within 4Å: Chain D: N.400, T.402, Q.428 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.402 NAG.35: 5 residues within 4Å: Chain G: E.110, N.114 Chain H: Y.32, Y.119 Chain I: P.58 6 PLIP interactions: 4 interactions with chain H, 1 interactions with chain I, 1 interactions with chain G Hydrogen bonds: H:Y.32, H:Y.32, H:Y.119, H:Y.119 Hydrophobic interactions: I:P.58, G:E.110 NAG.36: 2 residues within 4Å: Chain J: R.208, N.213 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:R.208 NAG.37: 4 residues within 4Å: Chain J: N.311, G.421, E.422 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.34 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.421 NAG.38: 3 residues within 4Å: Chain J: N.400, T.402, Q.428 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:T.402 NAG.54: 5 residues within 4Å: Chain M: E.110, N.114 Chain N: Y.32, Y.119 Chain O: P.58 6 PLIP interactions: 4 interactions with chain N, 1 interactions with chain O, 1 interactions with chain M Hydrogen bonds: N:Y.32, N:Y.32, N:Y.119, N:Y.119 Hydrophobic interactions: O:P.58, M:E.110 NAG.55: 2 residues within 4Å: Chain P: R.208, N.213 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:R.208 NAG.56: 4 residues within 4Å: Chain P: N.311, G.421, E.422 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.53 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.421 NAG.57: 3 residues within 4Å: Chain P: N.400, T.402, Q.428 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:T.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., Structural characterization of a highly-potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1 envelope. Nat Commun (2018)

Release Date

2018-05-02

Peptides

Envelope glycoprotein gp41: AGM
35O22 Heavy Chain: BHN
35O22 Light Chain: CIO
Envelope glycoprotein gp120: DJP
BG18 Heavy Chain: EKQ
BG18 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
Q

K
Q

Q
Q

F
R

L
R

R
R

Envelope glycoprotein gp41

35O22 Heavy Chain

35O22 Light Chain

Envelope glycoprotein gp120

BG18 Heavy Chain

BG18 Light Chain

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