SMTL ID : 5v7j.1

Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.91 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: 5 residues within 4Å: Chain A: N.121, K.132 Chain M: D.128 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.17, NAG-NAG-BMA-MAN-MAN-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.17: 5 residues within 4Å: Chain A: D.128 Chain G: N.121, K.132 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.33: 5 residues within 4Å: Chain G: D.128 Chain M: N.121, K.132 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.17 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: 18 residues within 4Å: Chain A: E.56, N.57 Chain B: S.17 Chain E: N.30, F.31, H.33, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, S.113, T.115 Chain F: H.95, N.96 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:H.95, E:T.115, E:D.111, E:D.111, E:S.113, E:S.113, E:H.33, E:S.52, E:D.57 Hydrophobic interactions: E:F.31 NAG-NAG-BMA-MAN-MAN-MAN-MAN.18: 18 residues within 4Å: Chain G: E.56, N.57 Chain H: S.17 Chain K: N.30, F.31, H.33, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, S.113, T.115 Chain L: H.95, N.96 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:T.115, L:H.95, K:D.111, K:D.111, K:S.113, K:S.113, K:H.33, K:S.52, K:D.57 Hydrophobic interactions: K:F.31 NAG-NAG-BMA-MAN-MAN-MAN-MAN.34: 18 residues within 4Å: Chain M: E.56, N.57 Chain N: S.17 Chain Q: N.30, F.31, H.33, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, S.113, T.115 Chain R: H.95, N.96 5 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:T.115, R:H.95, Q:D.111, Q:D.111, Q:S.113, Q:S.113, Q:H.33, Q:S.52, Q:D.57 Hydrophobic interactions: Q:F.31

6 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.3: 6 residues within 4Å: Chain A: Q.262, N.264, N.300, V.301, S.302, R.411 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.262 NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 4 residues within 4Å: Chain A: N.203, T.205, S.243, I.246 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 6 residues within 4Å: Chain G: Q.262, N.264, N.300, V.301, S.302, R.411 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.262 NAG-NAG-BMA-MAN-MAN-MAN-MAN.22: 4 residues within 4Å: Chain G: N.203, T.205, S.243, I.246 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.35: 6 residues within 4Å: Chain M: Q.262, N.264, N.300, V.301, S.302, R.411 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:Q.262 NAG-NAG-BMA-MAN-MAN-MAN-MAN.38: 4 residues within 4Å: Chain M: N.203, T.205, S.243, I.246 No protein-ligand interaction detected (PLIP)

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.4: 3 residues within 4Å: Chain A: N.102, I.107, K.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain B: E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain G: N.102, I.107, K.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 2 residues within 4Å: Chain H: E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 3 residues within 4Å: Chain M: N.102, I.107, K.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.45: 2 residues within 4Å: Chain N: E.123, N.126 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.5: 10 residues within 4Å: Chain A: T.104, N.117, S.119, Y.134, D.289 Chain C: G.23, R.24, Q.25, R.72, R.96 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.7: 11 residues within 4Å: Chain A: T.32, E.33, S.178, E.180, P.181, L.230, N.231, G.347, V.413, S.414 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.347 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.21: 10 residues within 4Å: Chain G: T.104, N.117, S.119, Y.134, D.289 Chain I: G.23, R.24, Q.25, R.72, R.96 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.23: 11 residues within 4Å: Chain G: T.32, E.33, S.178, E.180, P.181, L.230, N.231, G.347, V.413, S.414 Ligands: NAG-NAG.28 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.347 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.37: 10 residues within 4Å: Chain M: T.104, N.117, S.119, Y.134, D.289 Chain O: G.23, R.24, Q.25, R.72, R.96 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.39: 11 residues within 4Å: Chain M: T.32, E.33, S.178, E.180, P.181, L.230, N.231, G.347, V.413, S.414 Ligands: NAG-NAG.44 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:G.347

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.8: 3 residues within 4Å: Chain A: N.270, I.291, V.409 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.24: 3 residues within 4Å: Chain G: N.270, I.291, V.409 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.40: 3 residues within 4Å: Chain M: N.270, I.291, V.409 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-(1-6)-[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-MAN-MAN-MAN-MAN.9: 16 residues within 4Å: Chain A: H.298, N.300, N.378, T.382, R.411 Chain C: S.29, N.49, Q.51, P.65, D.66, I.67 Chain D: K.102, R.103, I.104, G.106, M.107 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.25: 16 residues within 4Å: Chain G: H.298, N.300, N.378, T.382, R.411 Chain I: S.29, N.49, Q.51, P.65, D.66, I.67 Chain J: K.102, R.103, I.104, G.106, M.107 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.41: 16 residues within 4Å: Chain M: H.298, N.300, N.378, T.382, R.411 Chain O: S.29, N.49, Q.51, P.65, D.66, I.67 Chain P: K.102, R.103, I.104, G.106, M.107 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.10: 2 residues within 4Å: Chain A: N.354, S.356 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.26: 2 residues within 4Å: Chain G: N.354, S.356 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.42: 2 residues within 4Å: Chain M: N.354, S.356 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.11: 3 residues within 4Å: Chain A: S.356, G.357, N.360 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: N.231, P.260, N.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain G: S.356, G.357, N.360 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain G: N.231, P.260, N.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.23 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 3 residues within 4Å: Chain M: S.356, G.357, N.360 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 4 residues within 4Å: Chain M: N.231, P.260, N.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.39 No protein-ligand interaction detected (PLIP)

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

NAG.14: 4 residues within 4Å: Chain A: G.322, N.323, N.324, S.430 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.323, A:S.430 NAG.15: 1 residues within 4Å: Chain B: N.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.100 NAG.16: 6 residues within 4Å: Chain B: N.105, N.107, E.110 Chain F: E.55, R.56, P.58 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:E.55 Hydrogen bonds: F:E.55, F:R.56, B:N.105 NAG.30: 4 residues within 4Å: Chain G: G.322, N.323, N.324, S.430 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.323, G:S.430 NAG.31: 1 residues within 4Å: Chain H: N.100 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.100 NAG.32: 6 residues within 4Å: Chain H: N.105, N.107, E.110 Chain L: E.55, R.56, P.58 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain H Hydrophobic interactions: L:E.55 Hydrogen bonds: L:E.55, L:R.56, H:N.105 NAG.46: 4 residues within 4Å: Chain M: G.322, N.323, N.324, S.430 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:N.323, M:S.430 NAG.47: 1 residues within 4Å: Chain N: N.100 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:N.100 NAG.48: 6 residues within 4Å: Chain N: N.105, N.107, E.110 Chain R: E.55, R.56, P.58 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain N Hydrophobic interactions: R:E.55 Hydrogen bonds: R:E.55, R:R.56, N:N.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Quantification of the Impact of the HIV-1-Glycan Shield on Antibody Elicitation. Cell Rep (2017)

Release Date

2017-06-21

Peptides

Envelope glycoprotein gp160: AGM
Envelope glycoprotein gp160: BHN
Antibody 3H+109L Fab light chain: CIO
Antibody 3H+109L Fab heavy chain: DJP
Antibody 35O22 Fab light chain: EKQ
Antibody 35O22 Fab heavy chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

G
G

M
G

B
B

H
B

N
B

C
L

I
L

O
L

D
H

J
H

P
H

E
D

K
D

Q
D

F
E

L
E

R
E

Envelope glycoprotein gp160

Envelope glycoprotein gp160

Antibody 3H+109L Fab light chain

Antibody 3H+109L Fab heavy chain

Antibody 35O22 Fab light chain

Antibody 35O22 Fab heavy chain

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