SMTL ID : 5t3x.1

3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.90 Å

Oligo State

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

Ligands

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

NAG-FUC.1: 4 residues within 4Å: Chain A: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.127, A:I.130 Hydrogen bonds: A:S.102 NAG-FUC.20: 4 residues within 4Å: Chain G: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.127, G:I.130 Hydrogen bonds: G:S.102 NAG-FUC.39: 4 residues within 4Å: Chain M: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:Y.127, M:I.130 Hydrogen bonds: M:S.102

3 x NAG- NAG- BMA- FUC: 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-FUC.2: 1 residues within 4Å: Chain A: N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.21: 1 residues within 4Å: Chain G: N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.40: 1 residues within 4Å: Chain M: N.126 No protein-ligand interaction detected (PLIP)

3 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.3: 5 residues within 4Å: Chain A: T.18, D.113, N.114 Chain B: E.57, N.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.113, A:N.114 NAG-NAG-FUC.22: 5 residues within 4Å: Chain G: T.18, D.113, N.114 Chain H: E.57, N.58 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.113, G:N.114 NAG-NAG-FUC.41: 5 residues within 4Å: Chain M: T.18, D.113, N.114 Chain N: E.57, N.58 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:D.113, M:N.114

3 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: 5 residues within 4Å: Chain B: N.103, D.110, G.114, R.140, K.159 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.111 NAG-NAG-BMA.23: 5 residues within 4Å: Chain H: N.103, D.110, G.114, R.140, K.159 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.111 NAG-NAG-BMA.42: 5 residues within 4Å: Chain N: N.103, D.110, G.114, R.140, K.159 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:D.111

3 x NAG- NAG- BMA- MAN- NAG- GAL- NAG- MAN- NAG- GAL- NAG- GAL- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]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-NAG-GAL-NAG-GAL-FUC.5: 5 residues within 4Å: Chain B: T.105, N.118, S.120, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-GAL-NAG-MAN-NAG-GAL-NAG-GAL-FUC.24: 5 residues within 4Å: Chain H: T.105, N.118, S.120, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-GAL-NAG-MAN-NAG-GAL-NAG-GAL-FUC.43: 5 residues within 4Å: Chain N: T.105, N.118, S.120, Y.135, D.290 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG- GAL- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-MAN-NAG-GAL-FUC.6: 5 residues within 4Å: Chain B: Q.100, S.120, F.121, N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-GAL-FUC.25: 5 residues within 4Å: Chain H: Q.100, S.120, F.121, N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-GAL-FUC.44: 5 residues within 4Å: Chain N: Q.100, S.120, F.121, N.122, K.131 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- NAG- GAL- SIA- MAN- NAG: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-GAL-SIA-MAN-NAG.7: 6 residues within 4Å: Chain B: R.162, N.167 Chain E: D.73, M.76, Y.80 Chain N: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG.26: 6 residues within 4Å: Chain B: R.278 Chain H: R.162, N.167 Chain K: D.73, M.76, Y.80 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG.45: 6 residues within 4Å: Chain H: R.278 Chain N: R.162, N.167 Chain Q: D.73, M.76, Y.80 No protein-ligand interaction detected (PLIP)

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.8: 7 residues within 4Å: Chain B: E.62, N.204, T.206, P.208, S.244, E.245 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-SIA-NAG-MAN-NAG-GAL-SIA-NAG-GAL-NAG-FUC.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.62 NAG-NAG.11: 4 residues within 4Å: Chain B: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain B: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 7 residues within 4Å: Chain H: E.62, N.204, T.206, P.208, S.244, E.245 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-SIA-NAG-MAN-NAG-GAL-SIA-NAG-GAL-NAG-FUC.29 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:E.62 NAG-NAG.30: 4 residues within 4Å: Chain H: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 1 residues within 4Å: Chain H: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 7 residues within 4Å: Chain N: E.62, N.204, T.206, P.208, S.244, E.245 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-SIA-NAG-MAN-NAG-GAL-SIA-NAG-GAL-NAG-FUC.48 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:E.62 NAG-NAG.49: 4 residues within 4Å: Chain N: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 1 residues within 4Å: Chain N: N.324 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-(1-6)]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.9: 14 residues within 4Å: Chain B: E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, I.407, R.412, C.413, V.414, S.415 Chain K: E.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.28: 14 residues within 4Å: Chain H: E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, I.407, R.412, C.413, V.414, S.415 Chain Q: E.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.47: 14 residues within 4Å: Chain E: E.1 Chain N: E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, I.407, R.412, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- NAG- GAL- SIA- NAG- MAN- NAG- GAL- SIA- NAG- GAL- NAG- FUC: N-acetyl-alpha-neuraminic acid-(2-6)-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)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]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-SIA-NAG-MAN-NAG-GAL-SIA-NAG-GAL-NAG-FUC.10: 8 residues within 4Å: Chain B: N.246, T.248, N.249 Chain E: S.108 Chain F: G.31, F.32, D.33 Ligands: NAG-NAG.8 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: E:S.108, F:D.33 Hydrophobic interactions: B:N.249 NAG-NAG-BMA-MAN-NAG-GAL-SIA-NAG-MAN-NAG-GAL-SIA-NAG-GAL-NAG-FUC.29: 8 residues within 4Å: Chain H: N.246, T.248, N.249 Chain K: S.108 Chain L: G.31, F.32, D.33 Ligands: NAG-NAG.27 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: H:N.249 Hydrogen bonds: K:S.108, L:D.33 NAG-NAG-BMA-MAN-NAG-GAL-SIA-NAG-MAN-NAG-GAL-SIA-NAG-GAL-NAG-FUC.48: 8 residues within 4Å: Chain N: N.246, T.248, N.249 Chain Q: S.108 Chain R: G.31, F.32, D.33 Ligands: NAG-NAG.46 3 PLIP interactions: 1 interactions with chain N, 1 interactions with chain Q, 1 interactions with chain R Hydrophobic interactions: N:N.249 Hydrogen bonds: Q:S.108, R:D.33

3 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-MAN-NAG.12: 8 residues within 4Å: Chain B: N.271, I.292, Q.408, G.409 Chain D: G.66, T.67, R.68 Chain K: Q.118 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN-NAG.31: 8 residues within 4Å: Chain H: N.271, I.292, Q.408, G.409 Chain J: G.66, T.67, R.68 Chain Q: Q.118 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN-NAG.50: 8 residues within 4Å: Chain E: Q.118 Chain N: N.271, I.292, Q.408, G.409 Chain P: G.66, T.67, R.68 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.13: 24 residues within 4Å: Chain B: N.265, T.267, D.294, R.296, N.301, T.383 Chain C: R.99, R.100, G.101, Q.102, R.103, I.104, Y.105, G.106, V.107, Y.116 Chain D: S.25, N.45, N.46, Q.47, D.48, P.61, D.62, N.64 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:V.108, B:R.296, C:R.103 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.32: 24 residues within 4Å: Chain H: N.265, T.267, D.294, R.296, N.301, T.383 Chain I: R.99, R.100, G.101, Q.102, R.103, I.104, Y.105, G.106, V.107, Y.116 Chain J: S.25, N.45, N.46, Q.47, D.48, P.61, D.62, N.64 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:R.296, I:V.108, I:R.103 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.51: 24 residues within 4Å: Chain N: N.265, T.267, D.294, R.296, N.301, T.383 Chain O: R.99, R.100, G.101, Q.102, R.103, I.104, Y.105, G.106, V.107, Y.116 Chain P: S.25, N.45, N.46, Q.47, D.48, P.61, D.62, N.64 2 PLIP interactions: 1 interactions with chain N, 1 interactions with chain O Hydrogen bonds: N:R.296, O:V.108, O:R.103

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.15: 6 residues within 4Å: Chain B: N.332, N.355, S.357 Chain E: R.85 Ligands: NAG-NAG-BMA-MAN-MAN.16, NAG-NAG-BMA-MAN-MAN.16 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.85, E:R.85 NAG-NAG-BMA-MAN-MAN-MAN-MAN.34: 6 residues within 4Å: Chain H: N.332, N.355, S.357 Chain K: R.85 Ligands: NAG-NAG-BMA-MAN-MAN.35, NAG-NAG-BMA-MAN-MAN.35 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.85, K:R.85 NAG-NAG-BMA-MAN-MAN-MAN-MAN.53: 6 residues within 4Å: Chain N: N.332, N.355, S.357 Chain Q: R.85 Ligands: NAG-NAG-BMA-MAN-MAN.54, NAG-NAG-BMA-MAN-MAN.54 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:R.85, Q:R.85

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.16: 4 residues within 4Å: Chain B: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.15, NAG-NAG-BMA-MAN-MAN-MAN-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.35: 4 residues within 4Å: Chain H: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.34, NAG-NAG-BMA-MAN-MAN-MAN-MAN.34 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.54: 4 residues within 4Å: Chain N: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.53, NAG-NAG-BMA-MAN-MAN-MAN-MAN.53 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- FUC: 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-MAN-FUC.17: 2 residues within 4Å: Chain B: N.361, T.363 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.36: 2 residues within 4Å: Chain H: N.361, T.363 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.55: 2 residues within 4Å: Chain N: N.361, T.363 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.18: 3 residues within 4Å: Chain B: P.261, Q.263, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.37: 3 residues within 4Å: Chain H: P.261, Q.263, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.56: 3 residues within 4Å: Chain N: P.261, Q.263, N.416 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain B: N.308, W.364 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.364 Hydrogen bonds: B:N.308 NAG.38: 2 residues within 4Å: Chain H: N.308, W.364 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:W.364 Hydrogen bonds: H:N.308 NAG.57: 2 residues within 4Å: Chain N: N.308, W.364 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:W.364 Hydrogen bonds: N:N.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gristick, H.B. et al., Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-10-05

Peptides

Envelope glycoprotein gp160: AGM
Envelope glycoprotein gp160: BHN
10-1074 Heavy Chain: CIO
10-1074 Light Chain: DJP
IOMA Heavy Chain: EKQ
IOMA Light Chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

G
B

M
B

B
G

H
G

N
G

C
H

I
H

O
H

D
L

J
L

P
L

E
D

K
D

Q
D

F
E

L
E

R
E

Envelope glycoprotein gp160

Envelope glycoprotein gp160

10-1074 Heavy Chain

10-1074 Light Chain

IOMA Heavy Chain

IOMA Light Chain

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