SMTL ID : 9o4f.1

Pre-fusion Stabilized HERV-K Envelope Trimer Ectodomain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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.1: 9 residues within 4Å: Chain A: N.32, D.33, H.252, P.282, L.283, Q.284, D.319, S.320, T.321 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.282 NAG-NAG-BMA-MAN-MAN.6: 8 residues within 4Å: Chain B: N.32, D.33, H.252, P.282, L.283, Q.284, D.319, S.320 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.282 NAG-NAG-BMA-MAN-MAN.11: 7 residues within 4Å: Chain C: N.32, D.33, H.252, P.282, Q.284, D.319, S.320 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.282

9 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: Y.176, N.178, S.180, E.218 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: I.255, W.256, S.257, N.276, S.277, S.278 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: M.55, I.56, N.57, E.310, N.311 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.178, S.180, E.218 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain B: I.255, S.257, N.276, S.277, S.278 Ligands: NAG-NAG-BMA.8, NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: M.55, I.56, N.57, E.310, N.311 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: Y.176, N.178, S.180, E.218 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain C: I.255, W.256, S.257, N.276, S.277, S.278 Ligands: NAG-NAG-BMA.13, NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain C: M.55, I.56, N.57, E.310, N.311 No protein-ligand interaction detected (PLIP)

9 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.3: 5 residues within 4Å: Chain A: H.208, N.259, N.276 Ligands: NAG-NAG.4, NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain B: H.208, N.259, N.276 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain C: H.208, N.259, N.276 Ligands: NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 6 residues within 4Å: Chain D: I.9, M.10, T.18, D.38, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain A: R.345 Chain D: W.88, N.89 Chain F: H.139 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 5 residues within 4Å: Chain E: M.10, T.18, D.38, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 5 residues within 4Å: Chain B: R.345 Chain D: H.139 Chain E: N.34, W.88, N.89 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 6 residues within 4Å: Chain F: I.9, M.10, T.18, D.38, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 5 residues within 4Å: Chain C: R.345 Chain E: H.139 Chain F: N.34, W.88, N.89 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.18: 4 residues within 4Å: Chain D: N.101, S.103, E.104, K.127 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.127 NAG-NAG-BMA-FUC.21: 4 residues within 4Å: Chain E: N.101, S.103, E.104, K.127 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.127 NAG-NAG-BMA-FUC.24: 4 residues within 4Å: Chain F: N.101, S.103, E.104, K.127 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.127

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

NAG.25: 1 residues within 4Å: Chain A: N.4 No protein-ligand interaction detected (PLIP) NAG.26: 1 residues within 4Å: Chain B: N.4 No protein-ligand interaction detected (PLIP) NAG.27: 1 residues within 4Å: Chain C: N.4 No protein-ligand interaction detected (PLIP) NAG.28: 1 residues within 4Å: Chain D: N.120 No protein-ligand interaction detected (PLIP) NAG.29: 1 residues within 4Å: Chain E: N.120 No protein-ligand interaction detected (PLIP) NAG.30: 1 residues within 4Å: Chain F: N.120 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shek, J. et al., Human endogenous retrovirus K (HERV-K) envelope structures in pre- and post-fusion by Cryo-EM. To Be Published

Release Date

2025-07-30

Peptides

Surface protein: ABC
Transmembrane protein,Fibritin: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Surface protein

Transmembrane protein,Fibritin

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