SMTL ID : 8dok.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 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: 21 residues within 4Å: Chain A: K.212, 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.83, E.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.70, C:A.71, C:A.59, C:F.63, C:G.65, C:V.67, C:I.69, C:I.69, C:D.73 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.12: 20 residues within 4Å: Chain I: K.212, N.214, H.331 Chain K: T.19, 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, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.70, K:A.71, K:S.58, K:A.59, K:F.63, K:G.65, K:V.67, K:I.69, K:I.69, K:D.73

7 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: 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.5: 11 residues within 4Å: Chain A: D.191, P.192, L.241, N.242, N.355, C.356, R.357, C.417, L.418, S.419 Ligands: NAG.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.418 Hydrogen bonds: A:L.418 NAG-NAG-BMA.6: 13 residues within 4Å: Chain B: N.126 Chain C: W.108, S.109 Chain D: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, L.56, G.57, A.67 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.53, D:L.55 NAG-NAG-BMA.10: 10 residues within 4Å: Chain E: D.191, L.241, N.242, N.355, C.356, R.357, C.417, L.418, S.419 Ligands: NAG.38 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.418 Hydrogen bonds: E:L.418 NAG-NAG-BMA.11: 11 residues within 4Å: Chain F: N.126 Chain G: W.108, S.109 Chain H: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, G.57 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:A.53, H:L.55 NAG-NAG-BMA.18: 11 residues within 4Å: Chain I: D.191, P.192, L.241, N.242, N.355, C.356, R.357, C.417, L.418, S.419 Ligands: NAG.54 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:L.418 NAG-NAG-BMA.19: 12 residues within 4Å: Chain J: N.126 Chain K: S.109 Chain L: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, L.56, G.57, A.67 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:L.55

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: 16 residues within 4Å: Chain A: T.277, Y.309, N.311, T.385, T.387, K.416 Chain M: R.103, I.104, Y.105, G.106, V.107, V.108 Chain N: N.45, D.62, I.63 Ligands: NAG.22 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:R.103, N:N.45, N:D.62 NAG-NAG-NAG-NAG.9: 13 residues within 4Å: Chain E: T.277, Y.309, N.311, T.385, T.387, K.416 Chain O: R.103, I.104, G.106, V.107, V.108 Chain P: D.62 Ligands: NAG.35 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:R.103 NAG-NAG-NAG-NAG.15: 17 residues within 4Å: Chain I: T.277, R.306, Y.309, N.311, T.385, T.387, K.416 Chain Q: R.103, I.104, Y.105, G.106, V.107, V.108 Chain R: N.45, Q.47, P.61, D.62 5 PLIP interactions: 3 interactions with chain R, 2 interactions with chain Q Hydrogen bonds: R:N.45, R:Q.47, R:Q.47, Q:R.103, Q:R.103

4 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.14: 6 residues within 4Å: Chain I: E.248, G.249, I.250, N.269, E.270, R.323 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain I: V.155, R.172, N.177, T.178 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain I: N.101, Y.146, F.168, E.170 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:F.168

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.7: 20 residues within 4Å: Chain E: K.212, N.214, H.331 Chain G: T.19, 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, 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- 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.8: 11 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, Q.124 Chain H: K.43 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.1, G:Q.1

1 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.13: 9 residues within 4Å: Chain I: N.256, T.258, N.259 Chain K: Q.1, H.3, Y.25, G.26, V.27, N.28 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Q.1, K:Q.1

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

NAG.20: 1 residues within 4Å: Chain A: N.133 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.221 Ligand excluded by PLIP NAG.22: 8 residues within 4Å: Chain A: K.273, N.275, N.311, I.312, S.313, T.385, L.418 Ligands: NAG-NAG-NAG-NAG.3 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.281, I.302 Chain N: F.65 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.242, S.271, N.420 Ligands: NAG-NAG-BMA.5 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: N.129, Y.146, L.148, G.299, D.300 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: E.248, I.250, N.269, R.323 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: T.366, N.370 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: V.155, R.172, N.177 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.101, F.168, E.170 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.105 Chain D: Q.27 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.113, N.114 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: K.87, N.88 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: N.133 Chain I: D.140 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: H.56, N.209, N.221 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain E: N.275, N.311, I.312, S.313, T.385, L.418 Ligands: NAG-NAG-NAG-NAG.9 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: N.281, N.282, I.302 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain E: N.334 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: S.271, N.420 Ligands: NAG-NAG-BMA.10 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain E: N.129, Y.146, L.148, D.300 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain E: E.248, G.249, I.250, N.269, E.270, R.323 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: M.351, N.364, T.366 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain E: N.370 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: V.155, R.172, N.177 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.101, F.168 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain F: P.98, N.100, S.102, W.103, I.134 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain F: S.101, N.105 Chain H: S.28 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: S.17, N.88 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain I: N.133 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain I: N.209, N.221 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain I: N.275, N.311, I.312, S.313, T.385, L.418 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain I: N.281, V.414 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain I: K.329, N.334 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain I: L.245, S.271, N.420 Ligands: NAG-NAG-BMA.18 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain I: N.129, Y.146, L.148, D.300 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain I: T.350, M.351, N.364, T.366 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain I: N.370 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain J: P.98, N.100, W.103, I.134 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain J: N.105 Chain L: Q.27 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain J: N.113, N.114 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain K: G.15, R.66, 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

2023-07-19

Peptides

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

CRF-1_AE T/F100 Env gp120

CRF-1_AE T/F100 HIV-1 gp41

Heavy chain of 8ANC195

Light chain of 8ANC195

Heavy chain of 10-1074

Light chain of 10-1074

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