SMTL ID : 8x0l.1

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

6 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: 3 residues within 4Å: Chain B: N.200 Chain C: C.63, F.95 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: L.260, D.261, N.262 Chain C: H.116, N.264 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain E: N.200 Chain F: F.95 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain E: L.260, D.261, N.262 Chain F: H.116, N.264 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain H: N.200 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain H: L.260, D.261, N.262 Chain I: H.116, N.264 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain C: R.134, M.136, N.141 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.134, C:N.141 NAG.8: 3 residues within 4Å: Chain F: R.134, M.136, N.141 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.134, F:N.141 NAG.9: 2 residues within 4Å: Chain I: M.136, N.141 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.141, I:N.141

3 x CA: CALCIUM ION(Non-covalent)

CA.10: 6 residues within 4Å: Chain J: W.20, D.23, E.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:W.20, J:E.25, J:D.27, J:D.33, J:E.34 CA.11: 7 residues within 4Å: Chain K: W.20, C.22, D.23, E.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:W.20, K:D.23, K:E.25, K:D.33, K:E.34 CA.12: 6 residues within 4Å: Chain L: W.20, D.23, E.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:W.20, L:E.25, L:D.27, L:D.33, L:E.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, F.G. et al., Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold). To Be Published

Release Date

2024-11-27

Peptides

Capsid protein: ADG
pike glycoprotein E2: BEH
pike glycoprotein E1: CFI
Very low-density lipoprotein receptor: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

G
I

B
B

E
F

H
J

C
C

F
G

I
K

J
H

K
D

L
L

Membrane

We predict this structure to be a membrane protein.
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Capsid protein

pike glycoprotein E2

pike glycoprotein E1

Very low-density lipoprotein receptor

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