SMTL ID : 6orn.1

Modified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch bNAb 10-1074

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.1: 7 residues within 4Å: Chain B: E.181, P.182, L.231, N.232, V.414, S.415 Ligands: NAG-NAG.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.414 NAG-NAG-BMA-MAN-MAN-MAN.11: 15 residues within 4Å: Chain D: T.267, H.299, N.301, S.381 Chain H: R.103, I.104, Y.105, G.106, V.107, V.108 Chain K: S.25, N.45, Q.47, D.62, I.63 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:V.108 NAG-NAG-BMA-MAN-MAN-MAN.16: 8 residues within 4Å: Chain F: V.224, L.231, N.232, N.346, Q.408, V.414, S.415 Ligands: NAG-NAG.21 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.181

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.2: 3 residues within 4Å: Chain B: E.245, N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 3 residues within 4Å: Chain B: T.342, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 1 residues within 4Å: Chain D: N.246 No protein-ligand interaction detected (PLIP)

2 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.3: 15 residues within 4Å: Chain B: T.267, H.299, N.301, V.383 Chain G: R.103, I.104, Y.105, G.106, V.107, V.108 Chain J: S.25, N.45, Q.47, D.62, I.63 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN.9: 6 residues within 4Å: Chain D: P.182, N.232, N.346, C.413, V.414 Ligands: NAG.37 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.414

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

NAG-NAG.5: 4 residues within 4Å: Chain B: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain D: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain D: T.342, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: S.17 Chain F: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain F: S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain F: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain F: N.246, I.247, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain F: N.271, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain F: T.342, N.355, S.357 Ligands: NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain F: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP)

1 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.19: 13 residues within 4Å: Chain F: T.267, H.299, N.301 Chain I: R.103, I.104, Y.105, G.106, V.107, V.108 Chain L: S.25, N.45, Q.47, D.62 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:V.108 Hydrogen bonds: I:V.108

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

NAG.22: 3 residues within 4Å: Chain A: K.122, E.123, N.126 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.107, E.110 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: S.17 Chain B: E.57, N.58 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: T.98, S.120, F.121, N.122 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: R.162, N.167 Chain F: R.278 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.204, T.206, E.245 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: Q.263, N.265, S.303, V.414 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.271 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.308 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.324 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: S.357, N.361 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.100, S.102 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.107 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: K.122, E.123, N.126 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain D: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.9 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain D: N.204, T.206, E.245 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: Q.263, N.265 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain D: N.271 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain D: N.308 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain D: G.323, N.324 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain D: S.357, N.361 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.100, S.102 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain E: N.107 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: K.122, E.123, N.126 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain F: N.204, T.206, S.244, E.245 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain F: Q.263, I.264, N.265 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain F: N.308 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain F: N.324 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain F: S.357, N.361 Ligands: NAG-NAG.20 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: ACE
RC1 variant of HIV-1 Env glycoprotein gp120: BDF
10-1074 antibody Fab heavy chain: GHI
10-1074 antibody Fab light chain: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
J

E
Q

B
G

D
K

F
R

G
A

H
F

I
O

J
B

K
I

L
P

RC1 variant of HIV-1 Env glycoprotein gp41

RC1 variant of HIV-1 Env glycoprotein gp120

10-1074 antibody Fab heavy chain

10-1074 antibody Fab light chain

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