SMTL ID : 6oro.1

Modified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch antibody Ab874NHP

Coordinates

PDB Format Compare

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: 1 residues within 4Å: Chain B: N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 1 residues within 4Å: Chain G: N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 1 residues within 4Å: Chain I: N.122 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.2: 5 residues within 4Å: Chain B: T.267, D.294, H.299, N.301 Chain D: G.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.294 NAG-NAG-BMA-MAN-MAN-MAN.11: 5 residues within 4Å: Chain G: T.267, D.294, H.299, N.301 Chain H: G.73 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.294 NAG-NAG-BMA-MAN-MAN-MAN.20: 5 residues within 4Å: Chain I: T.267, D.294, H.299, N.301 Chain J: G.73 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.294

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.3: 7 residues within 4Å: Chain B: E.181, L.231, N.232, N.346, V.414, S.415 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 7 residues within 4Å: Chain G: E.181, L.231, N.232, N.346, V.414, S.415 Ligands: NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.21: 7 residues within 4Å: Chain I: E.181, L.231, N.232, N.346, V.414, S.415 Ligands: NAG-NAG.22 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 4 residues within 4Å: Chain B: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: T.341, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.271 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain G: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain G: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain G: V.144, R.162, N.167 Chain I: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain G: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain G: T.341, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain G: N.271 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain I: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain I: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain B: R.278 Chain I: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain I: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain I: T.341, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 1 residues within 4Å: Chain I: N.271 No protein-ligand interaction detected (PLIP)

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

NAG.28: 1 residues within 4Å: Chain A: N.100 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.107, S.109, E.110 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.126 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: S.17 Chain B: E.57, N.58 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.308 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.324 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.246, T.248 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.100 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.107, S.109, E.110 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.126 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain F: N.100 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain F: N.126 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain F: N.107, S.109, E.110 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: S.17 Chain G: E.57, N.58 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain G: N.308 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: N.246, T.248 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain F: S.17 Chain I: E.57, N.58 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain I: N.308 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain I: N.246, T.248 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Escolano, A. et al., Immunization expands B cells specific to HIV-1 V3 glycan in mice and macaques. Nature (2019)

Release Date

2019-06-12

Peptides

RC1 variant of HIV-1 Env glycoprotein gp41: ACF
RC1 variant of HIV-1 Env glycoprotein gp120: BGI
Ab874NHP antibody Fab heavy chain: DHJ
Ab874NHP antibody Fab light chain: EKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

F
F

B
B

G
G

I
I

D
D

H
H

J
J

E
E

K
K

L
L

RC1 variant of HIV-1 Env glycoprotein gp41

RC1 variant of HIV-1 Env glycoprotein gp120

Ab874NHP antibody Fab heavy chain

Ab874NHP antibody Fab light chain

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