SMTL ID : 8ttw.1

Cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with temsavir, 8ANC195, and 10-1074

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

33 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: 7 residues within 4Å: Chain A: N.246, T.248, N.249 Chain C: Q.1, H.3, Y.25, G.26 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.3 NAG-NAG.2: 6 residues within 4Å: Chain B: N.126 Chain D: N.32, R.51, A.53, A.54, A.67 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.55 NAG-NAG.3: 8 residues within 4Å: Chain E: N.246, T.248, N.249 Chain G: Q.1, H.3, Y.25, G.26, N.28 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.3 NAG-NAG.4: 6 residues within 4Å: Chain F: N.126 Chain H: N.32, R.51, A.53, A.54, A.67 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:L.55 NAG-NAG.5: 7 residues within 4Å: Chain I: N.246, T.248, N.249 Chain K: Q.1, H.3, Y.25, G.26 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Q.1 NAG-NAG.6: 7 residues within 4Å: Chain J: N.126 Chain L: N.32, R.51, A.53, A.54, L.55, A.67 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:L.55 NAG-NAG.7: 3 residues within 4Å: Chain A: N.118, Y.135 Chain N: R.92 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: V.144, R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, S.381, R.412 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain A: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.16, NAG-NAG.16, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.15, NAG-NAG.15, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.15, NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain E: N.118, Y.135 Chain P: R.92 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain E: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain E: V.144, R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 7 residues within 4Å: Chain E: Q.263, N.265, N.301, S.303, S.381, R.412 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.26 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain E: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 7 residues within 4Å: Chain E: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.28, NAG-NAG.28, NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.27, NAG-NAG.27, NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain E: S.357, N.361 Ligands: NAG-NAG.27, NAG-NAG.28, NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.23 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain I: N.118, Y.135 Chain R: R.92 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 6 residues within 4Å: Chain I: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain A: R.278 Chain I: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 7 residues within 4Å: Chain I: Q.263, N.265, N.301, S.303, S.381, R.412 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.38 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 2 residues within 4Å: Chain I: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 7 residues within 4Å: Chain I: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.40, NAG-NAG.40, NAG-NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 5 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG-NAG.39, NAG-NAG.39, NAG-NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 4 residues within 4Å: Chain I: N.361 Ligands: NAG-NAG.39, NAG-NAG.40, NAG-NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 4 residues within 4Å: Chain I: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.35 No protein-ligand interaction detected (PLIP)

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.10: 21 residues within 4Å: Chain A: N.204, H.321 Chain C: T.19, I.52, W.55, S.57, S.58, A.59, R.64, 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:D.73, C:A.71 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.22: 20 residues within 4Å: Chain E: N.204 Chain G: T.19, I.52, W.55, S.57, S.58, A.59, R.64, 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 G Hydrogen bonds: G:D.73, G:A.71 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.34: 20 residues within 4Å: Chain I: N.204 Chain K: T.19, I.52, W.55, S.57, S.58, A.59, R.64, 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 K Hydrogen bonds: K:D.73, K:A.71

3 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.11: 9 residues within 4Å: Chain A: K.35, E.181, K.222, L.231, N.232, C.413, V.414, S.415 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 9 residues within 4Å: Chain E: K.35, E.181, K.222, L.231, N.232, C.413, V.414, S.415 Ligands: NAG-NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.35: 9 residues within 4Å: Chain I: K.35, E.181, K.222, L.231, N.232, C.413, V.414, S.415 Ligands: NAG-NAG.42 No protein-ligand interaction detected (PLIP)

3 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-(1-3)-[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.14: 18 residues within 4Å: Chain A: T.267, R.296, H.299, N.301 Chain M: R.103, I.104, Y.105, G.106, V.107, V.108 Chain N: S.25, N.45, N.46, Q.47, P.61, D.62, I.63 Ligands: NAG-NAG.12 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain A Hydrogen bonds: M:V.108, A:R.296, A:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.26: 19 residues within 4Å: Chain E: T.267, R.296, H.299, N.301, R.412 Chain O: R.103, I.104, Y.105, G.106, V.107, V.108 Chain P: S.25, N.45, N.46, Q.47, P.61, D.62, I.63 Ligands: NAG-NAG.24 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain O Hydrogen bonds: E:R.296, E:R.296, O:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.38: 19 residues within 4Å: Chain I: T.267, R.296, H.299, N.301, R.412 Chain Q: R.103, I.104, Y.105, G.106, V.107, V.108 Chain R: S.25, N.45, N.46, Q.47, P.61, D.62, I.63 Ligands: NAG-NAG.36 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain Q Hydrogen bonds: I:R.296, I:R.296, Q:V.108

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

NAG.43: 4 residues within 4Å: Chain A: N.103, N.106, M.112, N.158 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: K.320, N.324 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain A: N.58 Chain B: S.17 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain B: N.107, E.110 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.88 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain E: N.103, N.106, M.112, N.158 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain E: K.320, N.324 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain E: N.308, W.364 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, S.17 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain F: N.107, E.110 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain G: N.88 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain I: N.103, N.106, M.112, K.117, N.158 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain I: K.320, N.324 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain I: N.308, W.364 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain I: E.57, N.58 Chain J: G.16, S.17 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain J: N.107, E.110 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain K: N.88 Ligand excluded by PLIP

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.47: 19 residues within 4Å: Chain A: I.78, I.79, W.82, D.83, L.86, K.87, T.172, V.225, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, A.401, M.402 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.82, A:K.87, A:F.351, A:F.351, A:I.392, A:M.394, A:W.395 Hydrogen bonds: A:D.83, A:W.395 83J.55: 19 residues within 4Å: Chain E: I.78, I.79, W.82, D.83, L.86, K.87, T.172, V.225, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, A.401, M.402 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:W.82, E:K.87, E:F.351, E:F.351, E:I.392, E:M.394, E:W.395 Hydrogen bonds: E:D.83, E:W.395 83J.63: 17 residues within 4Å: Chain I: I.78, I.79, W.82, D.83, L.86, K.87, V.225, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, A.401, M.402 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:W.82, I:K.87, I:F.351, I:F.351, I:I.392, I:M.394, I:W.395 Hydrogen bonds: I:D.83, I:W.395

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

2023-11-08

Peptides

Envelope glycoprotein gp160: AEI
BG505 SOSIP.664 transmembrane protein gp41: BFJ
Antibody 8anc195 heavy chain: CGK
Antibody 8anc195 light chain: DHL
Antibody 10-1074 heavy chain: MOQ
Antibody 10-1074 light chain: 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

Envelope glycoprotein gp160

BG505 SOSIP.664 transmembrane protein gp41

Antibody 8anc195 heavy chain

Antibody 8anc195 light chain

Antibody 10-1074 heavy chain

Antibody 10-1074 light chain

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