SMTL ID : 6nqd.1

Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 21 residues within 4Å: Chain A: N.214, H.331 Chain C: T.19, W.55, S.57, S.58, A.59, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.82, S.83, E.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.70, C:S.70, C:A.71, C:A.71 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12: 21 residues within 4Å: Chain E: N.214, H.331 Chain G: T.19, W.55, S.57, S.58, A.59, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.82, S.83, E.85 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.70, G:S.70, G:A.71, G:A.71 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.23: 21 residues within 4Å: Chain I: N.214, H.331 Chain K: T.19, W.55, S.57, S.58, A.59, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.82, S.83, E.85 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.70, K:S.70, K:A.71, K:A.71

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.2: 8 residues within 4Å: Chain A: N.256, T.258, N.259 Chain C: Q.1, H.3, Y.25, G.26, N.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.1, C:Q.1 NAG-NAG-BMA-MAN-MAN-MAN.13: 8 residues within 4Å: Chain E: N.256, T.258, N.259 Chain G: Q.1, H.3, Y.25, G.26, N.28 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.1, G:Q.1 NAG-NAG-BMA-MAN-MAN-MAN.24: 8 residues within 4Å: Chain I: N.256, T.258, N.259 Chain K: Q.1, H.3, Y.25, G.26, N.28 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Q.1, K:Q.1

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.3: 4 residues within 4Å: Chain A: A.105, N.129, Y.146, I.301 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: E.248, G.249, I.250, N.269, E.270, K.319, R.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.323, A:R.323 NAG-NAG.5: 6 residues within 4Å: Chain A: T.277, Y.309, N.311, T.385, K.416 Ligands: NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: M.351, N.364, T.366 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: T.366, N.370 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: R.172, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.101 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: A.105, N.129, Y.146, I.301 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain E: E.248, G.249, I.250, N.269, E.270, K.319, R.323 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.323, E:R.323 NAG-NAG.16: 6 residues within 4Å: Chain E: T.277, Y.309, N.311, T.385, K.416 Ligands: NAG.46 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: M.351, N.364, T.366 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain E: T.366, N.370 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain E: R.172, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain E: N.101 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain I: A.105, N.129, Y.146, I.301 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 7 residues within 4Å: Chain I: E.248, G.249, I.250, N.269, E.270, K.319, R.323 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.323, I:R.323 NAG-NAG.27: 6 residues within 4Å: Chain I: T.277, Y.309, N.311, T.385, K.416 Ligands: NAG.56 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain I: M.351, N.364, T.366 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain I: T.366, N.370 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain I: R.172, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain I: N.101 No protein-ligand interaction detected (PLIP)

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.10: 6 residues within 4Å: Chain A: P.192, V.234, N.242, N.355, L.418, S.419 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 6 residues within 4Å: Chain E: P.192, V.234, N.242, N.355, L.418, S.419 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 6 residues within 4Å: Chain I: P.192, V.234, N.242, N.355, L.418, S.419 No protein-ligand interaction detected (PLIP)

3 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.11: 11 residues within 4Å: Chain B: N.126 Chain D: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, L.56, G.57, S.61 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.61, D:S.61, D:A.53, D:L.55 NAG-NAG-BMA-MAN.22: 11 residues within 4Å: Chain F: N.126 Chain H: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, L.56, G.57, S.61 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.61, H:S.61, H:A.53, H:L.55 NAG-NAG-BMA-MAN.33: 11 residues within 4Å: Chain J: N.126 Chain L: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, L.56, G.57, S.61 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:S.61, L:S.61, L:A.53, L:L.55

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

NAG.34: 2 residues within 4Å: Chain A: N.133, Q.142 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: H.56, N.209, N.221 Ligand excluded by PLIP NAG.36: 7 residues within 4Å: Chain A: K.273, N.275, N.311, I.312, S.313, L.418 Ligands: NAG-NAG.5 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.281 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.334 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: S.271, K.273, N.420 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: S.101, N.105 Chain D: S.28 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.113, N.114 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: G.15, N.88 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.133, Q.142 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: H.56, N.209, N.221 Ligand excluded by PLIP NAG.46: 7 residues within 4Å: Chain E: K.273, N.275, N.311, I.312, S.313, L.418 Ligands: NAG-NAG.16 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain E: N.281 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.334 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: S.271, K.273, N.420 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain F: S.101, N.105 Chain H: S.28 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain F: N.113, N.114 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain G: G.15, N.88 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain I: N.133, Q.142 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain I: H.56, N.209, N.221 Ligand excluded by PLIP NAG.56: 7 residues within 4Å: Chain I: K.273, N.275, N.311, I.312, S.313, L.418 Ligands: NAG-NAG.27 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain I: N.281 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain I: N.334 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain I: S.271, K.273, N.420 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain J: S.101, N.105 Chain L: S.28 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain J: N.113, N.114 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain K: G.15, N.88 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ananthaswamy, N. et al., A sequestered fusion peptide in the structure of an HIV-1 transmitted founder envelope trimer. Nat Commun (2019)

Release Date

2019-03-06

Peptides

T/F100 Env gp120: AEI
T/F100 Env gp41: BFJ
8ANC195 G52K5 heavy chain, IG gamma-1 chain: CGK
8ANC195 G52K5 light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

T/F100 Env gp120

T/F100 Env gp41

8ANC195 G52K5 heavy chain, IG gamma-1 chain

8ANC195 G52K5 light chain

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