SMTL ID : 8x0k.1

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-mer

Ligands

8 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: 4 residues within 4Å: Chain B: N.200, T.202 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: 4 residues within 4Å: Chain E: N.200, T.202, V.208 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: 4 residues within 4Å: Chain H: N.200, T.202, V.208 Chain I: F.95 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) NAG-NAG.7: 3 residues within 4Å: Chain K: N.200 Chain L: C.63, F.95 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain K: L.260, D.261, N.262 Chain L: H.116, N.264 No protein-ligand interaction detected (PLIP)

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

NAG.9: 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.10: 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.11: 2 residues within 4Å: Chain I: M.136, N.141 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain L: R.134, M.136, N.141 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.134, L:N.141

4 x CA: CALCIUM ION(Non-covalent)

CA.13: 8 residues within 4Å: Chain M: W.20, R.21, C.22, D.23, E.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:W.20, M:D.23, M:D.27, M:D.33, M:E.34 CA.14: 7 residues within 4Å: Chain N: W.20, D.23, E.25, N.26, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:D.23, N:E.25, N:D.27, N:D.33, N:D.33 CA.15: 6 residues within 4Å: Chain O: W.20, D.23, E.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.20, O:D.23, O:E.25, O:D.27, O:D.33 CA.16: 6 residues within 4Å: Chain P: W.20, D.23, E.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.20, P:E.25, P:D.27, P:D.33, P: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: ADGJ
Spike glycoprotein E2: BEHK
Spike glycoprotein E1: CFIL
Very low-density lipoprotein receptor: MNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

G
I

J
M

B
B

E
F

H
J

K
N

C
C

F
G

I
K

L
O

M
D

N
H

O
L

P
P

Membrane

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

Spike glycoprotein E2

Spike glycoprotein E1

Very low-density lipoprotein receptor

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