SMTL ID : 8czz.1

Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex with Temsavir, 8ANC195, and 10-1074

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.14 Å

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

2 x NAG- NAG- BMA- 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-(1-6)]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.1: 16 residues within 4Å: Chain A: N.214 Chain C: T.19, W.55, S.57, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, L.74, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.70, C:A.71, C:G.65, C:I.69, C:D.73 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.18: 17 residues within 4Å: Chain I: N.214 Chain K: I.52, W.55, S.57, S.58, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.70, K:A.71, K:A.59, K:G.65, K:I.69, K:I.69, K:D.73

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:Y.25, C:Q.1, C:Q.1 NAG-NAG-BMA-MAN-MAN-MAN.10: 9 residues within 4Å: Chain E: N.256, T.258, N.259 Chain G: Q.1, H.3, Y.25, G.26, V.27, N.28 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.1, G:Q.1 NAG-NAG-BMA-MAN-MAN-MAN.19: 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:Y.25, K:Q.1, K:Q.1

3 x NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-NAG.3: 11 residues within 4Å: Chain A: T.277, Y.309, N.311, T.387 Chain M: Q.102, R.103, I.104, G.106, V.107 Chain N: D.62, I.63 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: M:I.104 Hydrogen bonds: M:R.103, M:I.104, N:D.62 NAG-NAG-NAG-NAG.12: 11 residues within 4Å: Chain E: T.277, Y.309, N.311 Chain O: R.103, I.104, G.106, V.107, V.108 Chain P: Q.47, D.62, I.63 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain O Hydrogen bonds: P:Q.47, O:R.103 NAG-NAG-NAG-NAG.22: 11 residues within 4Å: Chain I: T.277, Y.309, N.311, T.387 Chain Q: R.103, I.104, Y.105, G.106, V.107, V.108 Chain R: D.62 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:R.103, R:D.62

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.4: 3 residues within 4Å: Chain A: M.351, N.364, T.366 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.370 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: V.155, R.172, N.177 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.155 NAG-NAG.11: 4 residues within 4Å: Chain E: N.129, Y.146, L.148, D.300 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: M.351, N.364, T.366 Ligands: NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain E: N.370 Ligands: NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain E: R.172, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain I: N.129, Y.146, L.148, D.300 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.300 NAG-NAG.21: 5 residues within 4Å: Chain I: E.248, G.249, I.250, N.269, R.323 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.323 NAG-NAG.23: 5 residues within 4Å: Chain I: T.350, M.351, N.364, T.366 Ligands: NAG.60 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain I: V.155, R.172, N.177, T.178 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.155 NAG-NAG.25: 2 residues within 4Å: Chain I: N.101, F.168 No protein-ligand interaction detected (PLIP)

5 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.7: 8 residues within 4Å: Chain A: D.191, N.242, N.355, R.357, C.417, L.418, S.419 Ligands: NAG.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.418 NAG-NAG-BMA.8: 9 residues within 4Å: Chain B: N.126 Chain D: N.32, Y.50, R.51, A.53, A.54, L.55, L.56, A.67 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.50 NAG-NAG-BMA.16: 7 residues within 4Å: Chain E: D.191, N.242, N.355, C.356, C.417, L.418, S.419 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:L.418 NAG-NAG-BMA.17: 9 residues within 4Å: Chain F: N.126 Chain H: N.32, Y.50, R.51, A.53, A.54, L.55, L.56, A.67 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Y.50, H:L.55 NAG-NAG-BMA.26: 7 residues within 4Å: Chain I: D.191, N.242, N.355, R.357, C.417, L.418, S.419 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:R.357, I:D.191, I:C.356, I:L.418

1 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.9: 17 residues within 4Å: Chain E: N.214 Chain G: T.19, W.55, S.57, S.58, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.70, G:A.71, G:D.73

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.27: 9 residues within 4Å: Chain J: N.126 Chain L: N.32, Y.50, R.51, A.53, A.54, L.55, L.56, A.67 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:Y.50, L:L.55

3 x 83J: 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol-1-yl)-1H-pyrrolo[2,3-c]pyridin-3-yl]ethane-1,2-dione(Non-covalent)

83J.28: 16 residues within 4Å: Chain A: I.80, W.83, D.84, L.87, K.182, V.235, S.353, F.360, Y.362, I.396, N.397, M.398, W.399, Q.404, A.405, M.406 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.182, A:V.235, A:F.360, A:I.396, A:W.399, A:Q.404 Hydrogen bonds: A:D.84, A:W.399 83J.46: 16 residues within 4Å: Chain E: I.80, W.83, D.84, L.87, K.182, V.235, S.353, F.354, Y.362, I.396, N.397, M.398, W.399, Q.404, A.405, M.406 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:K.182, E:V.235, E:Q.404 Hydrogen bonds: E:D.84, E:D.84, E:W.399 pi-Stacking: E:F.360 83J.59: 18 residues within 4Å: Chain I: I.80, W.83, D.84, L.87, K.182, V.235, S.353, F.354, F.360, Y.362, I.396, N.397, M.398, W.399, Q.404, A.405, M.406, M.448 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:K.182, I:V.235, I:F.360, I:Y.362, I:I.396, I:W.399 Hydrogen bonds: I:D.84, I:D.84, I:W.399

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

NAG.29: 2 residues within 4Å: Chain A: N.133 Ligands: NAG.36 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: H.56, N.221 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain A: N.275, I.312, S.313, T.385, L.418 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: N.281, N.282, T.283, I.302, K.412 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: N.242, S.271, N.420 Ligands: NAG-NAG-BMA.7 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: N.129, Y.146, L.148, D.300 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.269, R.323 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: N.101, F.168 Ligands: NAG.29 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.105 Chain D: Q.27 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.113, N.114 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: G.65, K.87, N.88 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain E: N.133 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: H.56, N.209, N.221 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain E: K.273, N.275, N.311, T.385, L.418 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: N.281, I.302 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain E: N.326, K.329, E.330, N.334 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain E: S.271, N.420 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: E.248, G.249, N.269 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain E: N.101, K.144, F.168 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain F: N.105 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain G: K.87, N.88 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain I: N.133 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain I: H.56, N.221 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain I: N.275, N.311, S.313, T.385, L.418 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain I: N.281, I.302, V.414 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain I: K.329, N.334 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain I: N.242, S.271, N.420 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain I: N.370 Ligands: NAG-NAG.23 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain J: P.98, N.100, I.134 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain J: N.105 Chain L: Q.27 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain J: N.113, N.114 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain K: G.65, N.88 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prevost, J. et al., Structure-function analyses reveal key molecular determinants of HIV-1 CRF01_AE resistance to the entry inhibitor temsavir. Nat Commun (2023)

Release Date

2023-05-31

Peptides

CRF01_AE T/F100 HIV-1 gp120: AEI
CRF-1_AE T/F100 HIV-1 gp41: BFJ
Heavy chain of 8ANC195 Fab: CGK
Light chain of 8ANC195 Fab: DHL
Heavy chain of 10-1074 Fab: MOQ
Light chain of 10-1074 Fab: NPR

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

M
M

O
O

Q
Q

N
N

P
P

R
R

CRF01_AE T/F100 HIV-1 gp120

CRF-1_AE T/F100 HIV-1 gp41

Heavy chain of 8ANC195 Fab

Light chain of 8ANC195 Fab

Heavy chain of 10-1074 Fab

Light chain of 10-1074 Fab

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