SMTL ID : 6ch7.1

XFEL crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- FUC: 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-FUC.1: 2 residues within 4Å: Chain A: K.122, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.18: 2 residues within 4Å: Chain G: K.122, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.35: 2 residues within 4Å: Chain M: K.122, N.126 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-FUC.2: 13 residues within 4Å: Chain A: G.16, S.17 Chain B: F.31, H.33, Y.54, R.110, D.111, G.112, S.113 Chain C: H.95, N.96 Chain D: E.57, N.58 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.57 NAG-NAG-BMA-MAN-NAG-GAL-MAN-FUC.19: 13 residues within 4Å: Chain G: G.16, S.17 Chain H: F.31, H.33, Y.54, R.110, D.111, G.112, S.113 Chain I: H.95, N.96 Chain J: E.57, N.58 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.57 NAG-NAG-BMA-MAN-NAG-GAL-MAN-FUC.36: 13 residues within 4Å: Chain M: G.16, S.17 Chain N: F.31, H.33, Y.54, R.110, D.111, G.112, S.113 Chain O: H.95, N.96 Chain P: E.57, N.58 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:E.57

3 x NAG- NAG- BMA- MAN- NAG- MAN- MAN- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN-MAN-FUC.3: 4 residues within 4Å: Chain D: T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN-MAN-FUC.20: 4 residues within 4Å: Chain J: T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN-MAN-FUC.37: 4 residues within 4Å: Chain P: T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP)

9 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: 4 residues within 4Å: Chain D: Q.100, N.122, K.133 Chain P: D.129 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain D: N.204, G.205, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 2 residues within 4Å: Chain D: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 4 residues within 4Å: Chain D: D.129 Chain J: Q.100, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 4 residues within 4Å: Chain J: N.204, G.205, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 2 residues within 4Å: Chain J: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 4 residues within 4Å: Chain J: D.129 Chain P: Q.100, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 4 residues within 4Å: Chain P: N.204, G.205, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.42 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 2 residues within 4Å: Chain P: N.271, I.292 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.5: 4 residues within 4Å: Chain D: V.144, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.22: 4 residues within 4Å: Chain J: V.144, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.39: 4 residues within 4Å: Chain P: V.144, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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.7: 13 residues within 4Å: Chain D: T.33, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.408 NAG-NAG-BMA-MAN-MAN-MAN-MAN.24: 13 residues within 4Å: Chain J: T.33, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.30 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Q.408 NAG-NAG-BMA-MAN-MAN-MAN-MAN.41: 13 residues within 4Å: Chain P: T.33, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.47 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:Q.408

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: 4 residues within 4Å: Chain D: N.246, T.248, N.249 Ligands: NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.25: 4 residues within 4Å: Chain J: N.246, T.248, N.249 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.42: 4 residues within 4Å: Chain P: N.246, T.248, N.249 Ligands: NAG-NAG-BMA.40 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.10: 2 residues within 4Å: Chain D: K.320, N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain J: K.320, N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 2 residues within 4Å: Chain P: K.320, N.324 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.11: 6 residues within 4Å: Chain D: N.355, S.357 Chain F: S.95 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN.12 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.95 NAG-NAG-BMA-MAN-MAN-MAN-MAN.28: 6 residues within 4Å: Chain J: N.355, S.357 Chain L: S.95 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.29, NAG-NAG-BMA-MAN-MAN-MAN-MAN.29, NAG-NAG-BMA-MAN-MAN-MAN-MAN.29 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.95 NAG-NAG-BMA-MAN-MAN-MAN-MAN.45: 6 residues within 4Å: Chain P: N.355, S.357 Chain R: S.95 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.46, NAG-NAG-BMA-MAN-MAN-MAN-MAN.46, NAG-NAG-BMA-MAN-MAN-MAN-MAN.46 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:S.95

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-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.12: 10 residues within 4Å: Chain D: N.361 Chain E: D.51, T.59, W.112, H.114 Chain F: D.96, S.97, Y.98 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.29: 10 residues within 4Å: Chain J: N.361 Chain K: D.51, T.59, W.112, H.114 Chain L: D.96, S.97, Y.98 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.28, NAG-NAG-BMA-MAN-MAN-MAN-MAN.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.46: 10 residues within 4Å: Chain P: N.361 Chain Q: D.51, T.59, W.112, H.114 Chain R: D.96, S.97, Y.98 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.45, NAG-NAG-BMA-MAN-MAN-MAN-MAN.45 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.13: 3 residues within 4Å: Chain D: N.232, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.30: 3 residues within 4Å: Chain J: N.232, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.47: 3 residues within 4Å: Chain P: N.232, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.41 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN.14: 13 residues within 4Å: Chain D: N.265, D.294, N.301 Chain E: S.28, R.29, H.33, R.102, I.103, Y.104, G.105, V.106 Chain F: S.52 Ligands: NAG.17 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.102, F:S.52 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.31: 13 residues within 4Å: Chain J: N.265, D.294, N.301 Chain K: S.28, R.29, H.33, R.102, I.103, Y.104, G.105, V.106 Chain L: S.52 Ligands: NAG.34 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:S.52, K:R.102 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.48: 13 residues within 4Å: Chain P: N.265, D.294, N.301 Chain Q: S.28, R.29, H.33, R.102, I.103, Y.104, G.105, V.106 Chain R: S.52 Ligands: NAG.51 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:R.102, R:S.52

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

NAG.15: 5 residues within 4Å: Chain A: N.105, N.107 Chain C: E.55 Chain D: E.2, R.468 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.2, A:N.107 NAG.16: 1 residues within 4Å: Chain D: N.103 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.103 NAG.17: 6 residues within 4Å: Chain D: Q.263, N.265, N.301, V.302, S.303 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.263, D:N.265, D:N.301 NAG.32: 5 residues within 4Å: Chain G: N.105, N.107 Chain I: E.55 Chain J: E.2, R.468 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain G Hydrogen bonds: J:E.2, G:N.107 NAG.33: 1 residues within 4Å: Chain J: N.103 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.103 NAG.34: 6 residues within 4Å: Chain J: Q.263, N.265, N.301, V.302, S.303 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.31 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:Q.263, J:N.265, J:N.301 NAG.49: 5 residues within 4Å: Chain M: N.105, N.107 Chain O: E.55 Chain P: E.2, R.468 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain P Hydrogen bonds: M:N.107, P:E.2 NAG.50: 1 residues within 4Å: Chain P: N.103 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.103 NAG.51: 6 residues within 4Å: Chain P: Q.263, N.265, N.301, V.302, S.303 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.48 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:Q.263, P:N.265, P:N.301

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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