SMTL ID : 9e9y.1

WEEV McMillan VLP in complex with VLDLR LA(1-2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.96 Å

Oligo State

hetero-4-4-4-4-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain G: K.227 Chain M: W.20, D.23, D.25, D.27, D.33 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:W.20, M:D.23, M:D.27, M:D.27, M:D.33 CA.2: 6 residues within 4Å: Chain M: W.59, D.62, D.64, D.66, D.72, E.73 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:W.59, M:D.62, M:D.64, M:D.66, M:D.72 CA.3: 6 residues within 4Å: Chain N: W.20, D.23, D.25, E.26, D.27, D.33 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.4: 8 residues within 4Å: Chain K: K.180 Chain N: W.59, D.62, D.64, P.65, D.66, D.72, E.73 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:W.59, N:D.62, N:D.64, N:D.66, N:D.72 CA.5: 7 residues within 4Å: Chain C: K.227 Chain O: W.20, D.23, D.25, E.26, D.27, D.33 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.20, O:D.25, O:D.27, O:D.27, O:D.33 CA.6: 7 residues within 4Å: Chain O: W.59, C.61, D.62, D.64, D.66, D.72, E.73 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.59, O:D.62, O:D.66, O:D.72, O:E.73 CA.7: 7 residues within 4Å: Chain A: K.227 Chain P: W.20, D.23, D.25, E.26, D.27, D.33 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.20, P:D.23, P:D.25, P:D.27, P:D.33 CA.8: 7 residues within 4Å: Chain B: K.180 Chain P: W.59, D.62, D.64, D.66, D.72, E.73 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.59, P:D.64, P:D.66, P:D.72, P:E.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raju, S. et al., Structural basis for plasticity in receptor engagement by an encephalitic alphavirus. Cell (2025)

Release Date

2025-04-23

Peptides

Spike glycoprotein E1: ACGJ
Structural polyprotein: BDHK
Capsid protein: EFIL
Very low-density lipoprotein receptor: MNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

G
G

J
J

B
B

D
D

H
H

K
K

E
E

F
F

I
I

L
L

M
V

N
X

O
Y

P
Z

Membrane

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

Structural polyprotein

Capsid protein

Very low-density lipoprotein receptor

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