SMTL ID : 8ihp.1

Structure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-3-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: K.198, N.200, T.202, N.207 Chain B: F.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.198, A:N.200, A:N.207 NAG.2: 4 residues within 4Å: Chain A: L.260, D.261, N.262 Chain B: H.116 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:H.116 Hydrogen bonds: B:H.116 NAG.3: 2 residues within 4Å: Chain B: M.136, N.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.141 NAG.4: 3 residues within 4Å: Chain D: N.200, N.207 Chain E: F.95 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.207 NAG.5: 4 residues within 4Å: Chain D: L.260, D.261, N.262 Chain E: H.116 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:D.261, D:N.262, E:H.116 NAG.6: 3 residues within 4Å: Chain E: R.134, M.136, N.141 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.134 NAG.7: 4 residues within 4Å: Chain G: N.200, N.207 Chain H: F.95, C.96 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.200 NAG.8: 4 residues within 4Å: Chain G: L.260, D.261, N.262 Chain H: H.116 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:H.116 NAG.9: 3 residues within 4Å: Chain H: R.134, M.136, N.141 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.134, H:R.134 NAG.10: 3 residues within 4Å: Chain J: N.200 Chain K: F.95, C.96 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.200 NAG.11: 4 residues within 4Å: Chain J: L.260, D.261, N.262 Chain K: H.116 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain K: M.136, N.141 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.141

3 x CA: CALCIUM ION(Non-covalent)

CA.13: 6 residues within 4Å: Chain M: W.22, D.25, E.27, D.29, D.35, E.36 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:W.22, M:D.25, M:E.27, M:D.29, M:E.36 CA.14: 7 residues within 4Å: Chain N: W.22, C.24, D.25, E.27, D.29, D.35, E.36 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:W.22, N:D.25, N:E.27, N:D.29, N:E.36 CA.15: 6 residues within 4Å: Chain O: W.22, D.25, E.27, D.29, D.35, E.36 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.22, O:D.25, O:E.27, O:D.29, O:E.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, D. et al., Structure of Semliki Forest virus in complex with its receptor VLDLR. Cell (2023)

Release Date

2023-04-12

Peptides

Spike glycoprotein E2: ADGJ
Spike glycoprotein E1: BEHK
Capsid protein: CFIL
Very low-density lipoprotein receptor: MNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
J

B
B

E
E

H
H

K
K

C
C

F
F

I
I

L
L

M
M

N
N

O
O

Membrane

We predict this structure to be a membrane protein.
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Spike glycoprotein E2

Spike glycoprotein E1

Capsid protein

Very low-density lipoprotein receptor