SMTL ID : 8ua8.1

Structure of Semliki Forest virus VLP in complex with VLDLR LA2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-1-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 A: R.134, M.136, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain E: R.134, M.136, N.141 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.134, E:R.134 NAG-NAG.5: 6 residues within 4Å: Chain E: C.63, F.95, E.99 Chain F: N.195, T.197, V.203 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.99 NAG-NAG.6: 3 residues within 4Å: Chain E: H.116, N.264 Chain F: N.257 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.264 NAG-NAG.7: 3 residues within 4Å: Chain I: R.134, M.136, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain M: R.134, M.136, N.141 No protein-ligand interaction detected (PLIP)

6 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.2: 4 residues within 4Å: Chain A: C.63, E.99 Chain B: N.195, V.203 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: H.116, N.264 Chain B: L.255, D.256, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain I: F.95, C.96, E.99 Chain J: N.195 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.99 NAG-NAG-BMA.9: 5 residues within 4Å: Chain I: H.116, N.264 Chain J: L.255, D.256, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain M: C.96 Chain N: N.195 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 6 residues within 4Å: Chain M: R.115, H.116, N.264 Chain N: L.255, D.256, N.257 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:R.115

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

NAG.13: 2 residues within 4Å: Chain G: A.7, N.8 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:A.7 Hydrogen bonds: G:N.8 NAG.14: 1 residues within 4Å: Chain K: N.8 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.15: 6 residues within 4Å: Chain Q: W.18, D.21, D.23, D.25, D.31, E.32 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:D.21, Q:D.23, Q:D.25, Q:D.31, Q:E.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abraham, J. et al., Cryo-EM structure of SFV VLP-VLDLRAD2 complex at the 3-fold axes. To Be Published

Release Date

2024-08-14

Peptides

Glycoprotein E1: AEIM
Glycoprotein E2: BFJN
Assembly protein E3: CGKO
Capsid protein: DHLP
Very low-density lipoprotein receptor: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

M
M

B
B

F
F

J
J

N
N

C
C

G
G

K
K

O
O

D
D

H
H

L
L

P
P

Q
R

Membrane

We predict this structure to be a membrane protein.
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Glycoprotein E1

Glycoprotein E2

Assembly protein E3

Capsid protein

Very low-density lipoprotein receptor

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