SMTL ID : 6orp.1

Modified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch antibody Ab897NHP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.40 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain B: Q.100, N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: R.162, I.164, N.167, T.168 Chain G: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.355, R.387 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: S.17 Chain G: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain G: N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain G: N.271 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain G: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain G: N.246, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain G: N.355 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 1 residues within 4Å: Chain I: N.271 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 6 residues within 4Å: Chain I: Q.332, T.342, C.354, N.355, S.357, R.387 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 1 residues within 4Å: Chain I: N.361 No protein-ligand interaction detected (PLIP)

10 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.3: 2 residues within 4Å: Chain B: N.204, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain B: H.299, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain B: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain G: N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain G: V.144, R.162, I.164, N.167, T.168 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.144 NAG-NAG-BMA.21: 3 residues within 4Å: Chain I: F.121, N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 5 residues within 4Å: Chain I: V.144, R.162, I.164, N.167, T.168 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:V.144, I:I.164 NAG-NAG-BMA.23: 1 residues within 4Å: Chain I: N.204 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 2 residues within 4Å: Chain I: T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 3 residues within 4Å: Chain I: H.299, N.301, R.412 No protein-ligand interaction detected (PLIP)

2 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.4: 6 residues within 4Å: Chain B: P.182, N.232, N.346, V.414, S.415 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.24: 7 residues within 4Å: Chain I: L.231, N.232, C.347, C.413, V.414, S.415 Ligands: NAG.51 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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.16: 6 residues within 4Å: Chain G: E.181, V.224, N.232, C.347, G.348, V.414 No protein-ligand interaction detected (PLIP)

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

NAG.30: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.107, E.110 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.126 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: S.17 Chain B: E.57, N.58 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Q.263, N.265 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.308, S.362, W.364 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.324 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.107, E.110 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.126 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: N.107, E.110 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain F: N.126 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: Q.263, N.265 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: K.304, N.308, E.309 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain G: N.361 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: P.261, N.416 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain F: S.17 Chain I: E.57, N.58 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain I: Q.263, N.265 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain I: K.304, N.308 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain I: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.24 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
Ab897NHP antibody Fab heavy chain: DHJ
Ab897NHP 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

Ab897NHP antibody Fab heavy chain

Ab897NHP antibody Fab light chain

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