SMTL ID : 8g6u.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- 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-(1-3)-[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-MAN-MAN.1: 20 residues within 4Å: Chain A: N.214, H.331 Chain C: T.19, I.52, 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, S.83, E.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.70, C:A.71, C:S.57, C:F.63, C:R.64, C:G.65, C:V.67, C:I.69, C:D.73 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.8: 20 residues within 4Å: Chain G: N.214, H.331 Chain I: T.19, I.52, 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, S.83, E.85 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.70, I:A.71, I:S.57, I:F.63, I:R.64, I:G.65, I:V.67, I:I.69, I:D.73 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.17: 18 residues within 4Å: Chain M: N.214, H.331 Chain O: T.19, I.52, W.55, S.57, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, S.83, E.85 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:S.57, O:F.63, O:R.64, O:G.65, O:I.69, O:D.73

6 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: 6 residues within 4Å: Chain A: N.256, N.259 Chain C: Q.1, H.3, Y.25, G.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.1, C:Y.25 NAG-NAG-BMA-MAN-MAN-MAN.6: 14 residues within 4Å: Chain A: E.33, V.36, K.187, S.189, D.191, L.241, N.242, N.355, C.356, R.357, C.417, L.418, S.419 Ligands: NAG-NAG.34 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.418 Hydrogen bonds: A:L.418 NAG-NAG-BMA-MAN-MAN-MAN.9: 6 residues within 4Å: Chain G: N.256, N.259 Chain I: Q.1, H.3, Y.25, G.26 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Q.1, I:Y.25 NAG-NAG-BMA-MAN-MAN-MAN.15: 14 residues within 4Å: Chain G: E.33, V.36, K.187, S.189, D.191, L.241, N.242, N.355, C.356, R.357, C.417, L.418, S.419 Ligands: NAG-NAG.35 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.418 Hydrogen bonds: G:L.418 NAG-NAG-BMA-MAN-MAN-MAN.18: 6 residues within 4Å: Chain M: N.256, N.259 Chain O: Q.1, H.3, Y.25, G.26 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:Q.1, O:Y.25 NAG-NAG-BMA-MAN-MAN-MAN.25: 14 residues within 4Å: Chain M: E.33, V.36, K.187, S.189, D.191, L.241, N.242, N.355, C.356, R.357, C.417, L.418, S.419 Ligands: NAG-NAG.36 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:L.418 Hydrogen bonds: M:L.418

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.3: 17 residues within 4Å: Chain A: R.306, Y.309, N.311, T.385, T.387 Chain E: Q.102, R.103, I.104, G.106, V.107, V.108 Chain F: N.45, N.46, Q.47, D.48, D.62, I.63 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:R.306, E:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11: 17 residues within 4Å: Chain G: R.306, Y.309, N.311, T.385, T.387 Chain K: Q.102, R.103, I.104, G.106, V.107, V.108 Chain L: N.45, N.46, Q.47, D.48, D.62, I.63 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain K Hydrogen bonds: G:R.306, K:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.21: 16 residues within 4Å: Chain M: R.306, Y.309, N.311, T.385 Chain Q: Q.102, R.103, I.104, G.106, V.107, V.108 Chain R: N.45, N.46, Q.47, D.48, D.62, I.63 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain Q Hydrogen bonds: M:R.306, Q:V.108

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.4: 3 residues within 4Å: Chain A: N.364, T.366 Ligands: NAG.45 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 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.10: 4 residues within 4Å: Chain G: N.129, Y.146, L.148, D.300 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: N.129, Y.146, L.148, D.300 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain G: N.364, T.366 Ligands: NAG.57 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain G: V.155, R.172, N.177 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.155 NAG-NAG.19: 4 residues within 4Å: Chain M: N.129, Y.146, L.148, D.300 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain M: E.248, N.269, R.323 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain M: N.364, T.366 Ligands: NAG.69 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain M: V.155, R.172, N.177 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:V.155 NAG-NAG.24: 5 residues within 4Å: Chain M: N.101, F.168, E.170 Ligands: NAG.62, NAG.63 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:F.168 NAG-NAG.27: 5 residues within 4Å: Chain A: N.101, F.168, E.170 Ligands: NAG.38, NAG.39 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.168 NAG-NAG.28: 4 residues within 4Å: Chain G: N.101, F.168, E.170 Ligands: NAG.50 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.168 NAG-NAG.29: 3 residues within 4Å: Chain A: E.248, N.269, R.323 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain G: E.248, N.269, R.323 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain A: H.56, N.209, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain G: H.56, N.209, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain M: H.56, N.209, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain A: S.271, N.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain G: S.271, N.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain M: S.271, N.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.25 No protein-ligand interaction detected (PLIP)

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.7: 13 residues within 4Å: Chain B: S.125, N.126 Chain C: W.108, S.109 Chain D: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, S.61, A.67 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.55 NAG-NAG-BMA-MAN-MAN.16: 13 residues within 4Å: Chain H: S.125, N.126 Chain I: W.108, S.109 Chain J: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, S.61, A.67 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:L.55 NAG-NAG-BMA-MAN-MAN.26: 13 residues within 4Å: Chain N: S.125, N.126 Chain O: W.108, S.109 Chain P: N.32, Y.50, R.51, G.52, A.53, A.54, L.55, S.61, A.67 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:L.55

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

NAG.37: 2 residues within 4Å: Chain A: N.59 Chain B: S.17 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.133 Ligands: NAG-NAG.27 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.167 Ligands: NAG-NAG.27 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain A: N.275, N.311, I.312, S.313, T.385 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: N.281, I.302, V.414 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain A: N.334 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain A: N.383 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: N.437, T.439 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain A: P.341, N.370 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: N.105 Chain D: Q.27 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: N.113, N.114 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain G: N.59 Chain H: S.17 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain G: N.133 Ligands: NAG-NAG.28 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain G: N.167 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain G: N.275, N.311, I.312, S.313, T.385 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: N.281, I.302, V.414 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain G: N.334 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain G: N.383 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain G: N.437, T.439 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain G: P.341, N.370 Ligands: NAG-NAG.13 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain H: N.100, S.102 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain H: N.105 Chain J: Q.27 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain H: N.113, N.114 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain M: N.59 Chain N: S.17 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain M: N.133 Ligands: NAG-NAG.24 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain M: N.167 Ligands: NAG-NAG.24 Ligand excluded by PLIP NAG.64: 5 residues within 4Å: Chain M: N.275, N.311, I.312, S.313, T.385 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain M: N.281, I.302, V.414 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain M: N.334 Ligand excluded by PLIP NAG.67: 1 residues within 4Å: Chain M: N.383 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain M: N.437, T.439 Ligand excluded by PLIP NAG.69: 3 residues within 4Å: Chain M: P.341, N.370 Ligands: NAG-NAG.22 Ligand excluded by PLIP NAG.70: 2 residues within 4Å: Chain N: N.100, S.102 Ligand excluded by PLIP NAG.71: 2 residues within 4Å: Chain N: N.105 Chain P: Q.27 Ligand excluded by PLIP NAG.72: 2 residues within 4Å: Chain N: N.113, N.114 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

2023-11-08

Peptides

CRF01_AE T/F100 HIV-1 gp120: AGM
CRF-1_AE T/F100 HIV-1 gp41: BHN
Heavy chain of 8ANC195: CIO
Light chain of 8ANC195: DJP
Heavy chain of 10-1074: EKQ
Light chain of 10-1074: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
E

M
I

B
B

H
F

N
J

C
C

I
G

O
K

D
D

J
H

P
L

E
M

K
O

Q
Q

F
N

L
P

R
R

CRF01_AE T/F100 HIV-1 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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