SMTL ID : 8ua4.1

Structure of eastern equine encephalitis virus VLP in complex with VLDLR LA1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.134, W.142, S.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.144, A:S.144 NAG.2: 2 residues within 4Å: Chain B: K.276, N.315 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.276 NAG.3: 3 residues within 4Å: Chain D: N.134, W.142, S.144 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.134 NAG.4: 3 residues within 4Å: Chain E: K.276, I.281, N.315 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.281 NAG.5: 3 residues within 4Å: Chain G: N.134, W.142, S.144 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:W.142 Hydrogen bonds: G:S.144 NAG.6: 2 residues within 4Å: Chain H: T.313, N.315 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain J: N.134, W.142, S.144 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:S.144, J:S.144 NAG.8: 4 residues within 4Å: Chain K: K.276, I.281, T.313, N.315 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.281 NAG.9: 1 residues within 4Å: Chain M: N.11 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain N: N.11 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:N.11 NAG.11: 1 residues within 4Å: Chain O: N.11 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain P: A.10, N.11 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 9 residues within 4Å: Chain K: K.156 Chain Q: W.18, K.19, C.20, D.21, D.23, D.25, D.31, E.32 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:W.18, Q:D.21, Q:D.31, Q:E.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, P. et al., Structural basis for VLDLR recognition by eastern equine encephalitis virus. Nat Commun (2024)

Release Date

2024-08-14

Peptides

Envelope glycoprotein E1: ADGJ
Envelope glycoprotein E2: BEHK
Capsid protein: CFIL
Envelope glycoprotein E3: MNOP
Very low-density lipoprotein receptor: Q

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

P
P

Q
R

Membrane

We predict this structure to be a membrane protein.
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Envelope glycoprotein E1

Envelope glycoprotein E2

Capsid protein

Envelope glycoprotein E3

Very low-density lipoprotein receptor

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