SMTL ID : 6did.1

HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 6 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, D.113 Chain K: S.26, Q.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 6 residues within 4Å: Chain C: E.57, N.58 Chain D: G.16, D.113 Chain G: S.26, Q.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 6 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, D.113 Chain I: S.26, Q.27 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: 4 residues within 4Å: Chain A: N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain A: N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: R.162, N.167 Chain E: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain C: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain E: N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain E: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain E: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain E: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain E: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain E: N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.29 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.5: 11 residues within 4Å: Chain A: E.181, P.182, K.222, V.224, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.181, A:G.348, A:V.414 NAG-NAG-BMA-MAN-MAN-MAN-MAN.17: 11 residues within 4Å: Chain C: E.181, P.182, K.222, V.224, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.181, C:G.348, C:V.414 NAG-NAG-BMA-MAN-MAN-MAN-MAN.29: 11 residues within 4Å: Chain E: E.181, P.182, K.222, V.224, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.36 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.181, E:G.348, E:V.414

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.6: 1 residues within 4Å: Chain A: N.246 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.18: 1 residues within 4Å: Chain C: N.246 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.30: 1 residues within 4Å: Chain E: N.246 No protein-ligand interaction detected (PLIP)

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.10: 4 residues within 4Å: Chain A: N.332, T.341 Ligands: NAG-NAG-BMA-MAN.11, NAG-NAG-BMA-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.22: 4 residues within 4Å: Chain C: N.332, T.341 Ligands: NAG-NAG-BMA-MAN.23, NAG-NAG-BMA-MAN.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.34: 4 residues within 4Å: Chain E: N.332, T.341 Ligands: NAG-NAG-BMA-MAN.35, NAG-NAG-BMA-MAN.35 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.11: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN-MAN.10, NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.22, NAG-NAG-BMA-MAN-MAN-MAN.22, NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.35: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.34, NAG-NAG-BMA-MAN-MAN-MAN.34, NAG.55 No protein-ligand interaction detected (PLIP)

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

NAG.37: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: K.202, N.204 Chain K: Y.32 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.308 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG-BMA-MAN.11 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.103 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: K.202, N.204 Chain G: Y.32 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG-BMA-MAN.23 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain D: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain E: K.202, N.204 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG-BMA-MAN.35 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain F: K.122, E.123, S.125, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bianchi, M. et al., Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization. Immunity (2018)

Release Date

2018-09-05

Peptides

Envelope glycoprotein gp160: ACE
Envelope glycoprotein gp160: BDF
Monoclonal antibody 10A light chain: GIK
Monoclonal antibody 10A heavy chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
F

E
G

B
B

D
I

F
J

G
C

I
E

K
H

H
D

J
K

L
L

Envelope glycoprotein gp160

Envelope glycoprotein gp160

Monoclonal antibody 10A light chain

Monoclonal antibody 10A heavy chain

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