SMTL ID : 7sfw.1

CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP in complex with Fab hVEEV-63 (focus refine of the asymmetric unit)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.134 NAG.2: 2 residues within 4Å: Chain B: N.212, K.213 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.213 Hydrogen bonds: B:N.212, B:K.213, B:K.213, B:K.213 NAG.3: 2 residues within 4Å: Chain B: S.284, N.318 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.284, B:N.318 NAG.4: 2 residues within 4Å: Chain D: T.32, N.134 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.32, D:N.134 NAG.5: 3 residues within 4Å: Chain E: N.212, K.213 Chain P: P.27 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:K.213 Hydrogen bonds: E:K.213, E:K.213 NAG.6: 3 residues within 4Å: Chain E: T.277, S.284, N.318 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.318 NAG.7: 4 residues within 4Å: Chain G: T.32, T.34, N.134, V.143 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:T.32 Hydrogen bonds: G:N.134 NAG.8: 2 residues within 4Å: Chain H: N.212, K.213 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:N.212, H:K.213 Hydrogen bonds: H:N.212, H:K.213, H:K.213 NAG.9: 3 residues within 4Å: Chain H: T.277, S.284, N.318 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.284 NAG.10: 4 residues within 4Å: Chain J: T.32, T.34, N.134, V.143 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:T.32 Hydrogen bonds: J:N.134 NAG.11: 2 residues within 4Å: Chain K: N.212, K.213 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:N.212, K:K.213 Hydrogen bonds: K:K.213, K:K.213 NAG.12: 3 residues within 4Å: Chain K: T.277, S.284, N.318 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kafai, N.M. et al., Neutralizing antibodies protect mice against Venezuelan equine encephalitis virus aerosol challenge. J.Exp.Med. (2022)

Release Date

2022-03-16

Peptides

Spike glycoprotein E1: ADGJ
Spike glycoprotein E2: BEHK
Capsid protein: CFIL
hVEEV-63 Fab heavy chain: MOQS
hVEEV-63 Fab light chain: NPRT

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

O
O

Q
Q

S
S

N
N

P
P

R
R

T
T

Membrane

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

Spike glycoprotein E2

Capsid protein

hVEEV-63 Fab heavy chain

hVEEV-63 Fab light chain

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