SMTL ID : 8xi5.1

Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA3-5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x CA: CALCIUM ION

CA.1: 7 residues within 4Å: Chain B: K.156 Chain M: W.20, D.23, D.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.25, M:D.27, M:D.33 CA.2: 6 residues within 4Å: Chain N: W.20, D.23, D.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:W.20, N:D.23, N:D.25, N:D.27, N:D.33 CA.3: 6 residues within 4Å: Chain O: W.20, D.23, D.25, D.27, D.33, E.34 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:W.20, O:D.23, O:D.25 CA.4: 6 residues within 4Å: Chain P: W.20, D.23, D.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.20, P:D.23, P:D.27, P:D.33, P:E.34 CA.5: 6 residues within 4Å: Chain Q: W.22, D.25, E.27, D.29, D.35, E.36 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:W.22, Q:D.25, Q:D.25, Q:D.29, Q:D.35 CA.6: 7 residues within 4Å: Chain B: K.206 Chain R: W.22, D.25, E.27, D.29, D.35, E.36 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:D.25, R:D.29, R:D.35 CA.7: 6 residues within 4Å: Chain S: W.22, D.25, E.27, D.29, D.35, E.36 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:W.22, S:D.25, S:D.25, S:D.29, S:D.35 CA.8: 5 residues within 4Å: Chain T: W.22, D.25, D.29, D.35, E.36 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:W.22, T:D.25, T:D.25, T:D.29, T:D.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, D. et al., The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes. Nat Commun (2024)

Release Date

2024-08-28

Peptides

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

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
Q

R
R

S
S

T
T

Membrane

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

Spike glycoprotein E2

Capsid protein

Very low-density lipoprotein receptor

Very low-density lipoprotein receptor

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