SMTL ID : 6mn7.1

Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

18 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: 4 residues within 4Å: Chain A: N.58 Chain B: G.16, S.17, T.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain A: N.246, T.248, N.249 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain A: N.332, T.341 Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA.13, NAG-NAG-BMA.13, NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain C: N.58 Chain E: G.16, S.17, T.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain C: N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain C: Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 4 residues within 4Å: Chain C: N.246, T.248, N.249 Ligands: NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 4 residues within 4Å: Chain C: N.332, T.341 Ligands: NAG-NAG-BMA.31, NAG-NAG-BMA.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG-BMA.30, NAG-NAG-BMA.30, NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 4 residues within 4Å: Chain D: N.58 Chain F: G.16, S.17, T.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 3 residues within 4Å: Chain D: N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 2 residues within 4Å: Chain D: Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 4 residues within 4Å: Chain D: N.246, T.248, N.249 Ligands: NAG-NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.46: 4 residues within 4Å: Chain D: N.332, T.341 Ligands: NAG-NAG-BMA.47, NAG-NAG-BMA.47 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.47: 5 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG-NAG-BMA.46, NAG-NAG-BMA.46, NAG-NAG.48 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: N.103, D.110 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.204, T.206, S.244 Ligands: NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain A: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain A: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: N.103, D.110 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.204, T.206, S.244 Ligands: NAG-NAG-BMA.25 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 1 residues within 4Å: Chain C: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG-BMA.31 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain C: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 2 residues within 4Å: Chain D: N.103, D.110 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 2 residues within 4Å: Chain D: I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain D: N.204, T.206, S.244 Ligands: NAG-NAG-BMA.41 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 1 residues within 4Å: Chain D: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 2 residues within 4Å: Chain D: N.361 Ligands: NAG-NAG-BMA.47 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 4 residues within 4Å: Chain D: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.40 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 2 residues within 4Å: Chain E: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.51: 2 residues within 4Å: Chain F: N.100, S.102 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-(1-3)-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.7: 6 residues within 4Å: Chain A: K.222, L.231, N.232, V.414, S.415 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.24: 6 residues within 4Å: Chain C: K.222, L.231, N.232, V.414, S.415 Ligands: NAG-NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.40: 6 residues within 4Å: Chain D: K.222, L.231, N.232, V.414, S.415 Ligands: NAG-NAG.49 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.9: 5 residues within 4Å: Chain A: N.265, N.301, R.412, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.26: 5 residues within 4Å: Chain C: N.265, N.301, R.412, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.42: 5 residues within 4Å: Chain D: N.265, N.301, R.412, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.44 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.10: 9 residues within 4Å: Chain A: N.271, I.292, Q.408, V.410 Chain G: T.28, T.30, H.54, T.74, S.75 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.27: 9 residues within 4Å: Chain C: N.271, I.292, Q.408, V.410 Chain I: T.28, T.30, H.54, T.74, S.75 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.43: 9 residues within 4Å: Chain D: N.271, I.292, Q.408, V.410 Chain H: T.28, T.30, H.54, T.74, S.75 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.11: 12 residues within 4Å: Chain A: C.300, N.301, N.379, S.381, I.382, T.383 Chain G: P.107, Y.110, A.157, Y.158, F.194 Ligands: NAG-NAG-BMA-MAN-MAN.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.379, A:T.383 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.28: 12 residues within 4Å: Chain C: C.300, N.301, N.379, S.381, I.382, T.383 Chain I: P.107, Y.110, A.157, Y.158, F.194 Ligands: NAG-NAG-BMA-MAN-MAN.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.379, C:T.383 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.44: 12 residues within 4Å: Chain D: C.300, N.301, N.379, S.381, I.382, T.383 Chain H: P.107, Y.110, A.157, Y.158, F.194 Ligands: NAG-NAG-BMA-MAN-MAN.42 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.379, D:T.383

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

NAG.52: 3 residues within 4Å: Chain A: K.304, N.308, W.364 No protein-ligand interaction detected (PLIP) NAG.53: 2 residues within 4Å: Chain B: N.105, N.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.107 NAG.54: 2 residues within 4Å: Chain B: E.123, N.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.126, B:N.126 NAG.55: 3 residues within 4Å: Chain C: K.304, N.308, W.364 No protein-ligand interaction detected (PLIP) NAG.56: 3 residues within 4Å: Chain D: K.304, N.308, W.364 No protein-ligand interaction detected (PLIP) NAG.57: 2 residues within 4Å: Chain E: N.105, N.107 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.107 NAG.58: 2 residues within 4Å: Chain E: E.123, N.126 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.126, E:N.126 NAG.59: 2 residues within 4Å: Chain F: N.105, N.107 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.107 NAG.60: 2 residues within 4Å: Chain F: E.123, N.126 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.126, F:N.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simonich, C.A. et al., Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage. Nat Commun (2019)

Release Date

2019-03-06

Peptides

Envelope Glycoprotein gp120: ACD
Envelope Glycoprotein gp41: BEF
BF520.1 Fab variable region: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

B
B

E
E

F
F

G
G

H
H

I
I

Envelope Glycoprotein gp120

Envelope Glycoprotein gp41

BF520.1 Fab variable region

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