SMTL ID : 6wxg.1

Cryo-EM reconstruction of VP5*/VP8* assembly from rhesus rotavirus particles - Reversed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-18-18-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain V: N.69 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain W: N.69 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain X: N.69 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain Y: N.69 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain Z: N.69 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain 0: N.69 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain 1: N.69 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain 2: N.69 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain 3: N.69 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain 4: N.69 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain 5: N.69 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain 6: N.69 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain 7: N.69 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain 8: N.69 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain 9: N.69 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain a: N.69 Ligand excluded by PLIP NAG.67: 1 residues within 4Å: Chain b: N.69 Ligand excluded by PLIP NAG.71: 1 residues within 4Å: Chain c: N.69 Ligand excluded by PLIP

54 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain V: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:D.151, V:E.154, V:E.222, V:L.224 CA.3: 8 residues within 4Å: Chain V: Q.177, D.179, E.180, K.183, D.228, V.229, D.231 Chain W: D.301 5 PLIP interactions: 4 interactions with chain V, 1 interactions with chain W Metal complexes: V:D.228, V:D.228, V:D.231, V:D.231, W:D.301 CA.4: 5 residues within 4Å: Chain V: G.206, C.207, T.214, E.216 Chain W: D.95 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain W Metal complexes: V:G.206, V:T.214, W:D.95 CA.5: 7 residues within 4Å: Chain V: D.301 Chain X: Q.177, E.180, K.183, D.228, V.229, D.231 5 PLIP interactions: 1 interactions with chain V, 4 interactions with chain X Metal complexes: V:D.301, X:D.228, X:D.228, X:D.231, X:D.231 CA.6: 5 residues within 4Å: Chain V: D.95 Chain X: G.206, C.207, T.214, E.216 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain V Metal complexes: X:G.206, X:T.214, V:D.95 CA.8: 6 residues within 4Å: Chain W: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:D.151, W:E.154, W:E.222, W:L.224 CA.9: 8 residues within 4Å: Chain W: Q.177, E.180, N.182, K.183, D.228, V.229, D.231 Chain X: D.301 4 PLIP interactions: 1 interactions with chain X, 3 interactions with chain W Metal complexes: X:D.301, W:D.228, W:D.228, W:D.231 CA.10: 5 residues within 4Å: Chain W: G.206, C.207, T.214, E.216 Chain X: D.95 3 PLIP interactions: 2 interactions with chain W, 1 interactions with chain X Metal complexes: W:G.206, W:T.214, X:D.95 CA.12: 6 residues within 4Å: Chain X: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:D.151, X:E.154, X:E.222, X:L.224 CA.14: 6 residues within 4Å: Chain Y: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:D.151, Y:E.154, Y:E.222, Y:L.224 CA.15: 5 residues within 4Å: Chain Y: Q.177, D.228, V.229, D.231 Chain Z: D.301 5 PLIP interactions: 1 interactions with chain Z, 4 interactions with chain Y Metal complexes: Z:D.301, Y:D.228, Y:D.228, Y:V.229, Y:D.231 CA.16: 5 residues within 4Å: Chain Y: G.206, C.207, T.214, E.216 Chain Z: D.95 3 PLIP interactions: 1 interactions with chain Z, 2 interactions with chain Y Metal complexes: Z:D.95, Y:G.206, Y:T.214 CA.17: 6 residues within 4Å: Chain 0: Q.177, E.180, D.228, V.229, D.231 Chain Y: D.301 4 PLIP interactions: 3 interactions with chain 0, 1 interactions with chain Y Metal complexes: 0:D.228, 0:D.228, 0:D.231, Y:D.301 CA.18: 5 residues within 4Å: Chain 0: G.206, C.207, T.214, E.216 Chain Y: D.95 3 PLIP interactions: 1 interactions with chain Y, 2 interactions with chain 0 Metal complexes: Y:D.95, 0:G.206, 0:T.214 CA.20: 6 residues within 4Å: Chain Z: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:D.151, Z:E.154, Z:E.222, Z:L.224 CA.21: 7 residues within 4Å: Chain 0: D.301, Y.302 Chain Z: Q.177, E.180, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain Z, 1 interactions with chain 0 Metal complexes: Z:D.228, Z:D.228, Z:V.229, Z:D.231, 0:D.301 CA.22: 5 residues within 4Å: Chain 0: D.95 Chain Z: G.206, C.207, T.214, E.216 3 PLIP interactions: 2 interactions with chain Z, 1 interactions with chain 0 Metal complexes: Z:G.206, Z:T.214, 0:D.95 CA.24: 6 residues within 4Å: Chain 0: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:D.151, 0:E.154, 0:E.222, 0:L.224 CA.26: 6 residues within 4Å: Chain 1: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:D.151, 1:E.154, 1:E.222, 1:L.224 CA.27: 5 residues within 4Å: Chain 1: Q.177, D.228, V.229, D.231 Chain 2: D.301 5 PLIP interactions: 4 interactions with chain 1, 1 interactions with chain 2 Metal complexes: 1:D.228, 1:D.228, 1:V.229, 1:D.231, 2:D.301 CA.28: 5 residues within 4Å: Chain 1: G.206, C.207, T.214, E.216 Chain 2: D.95 3 PLIP interactions: 2 interactions with chain 1, 1 interactions with chain 2 Metal complexes: 1:G.206, 1:T.214, 2:D.95 CA.29: 8 residues within 4Å: Chain 1: D.301 Chain 3: Q.177, D.179, E.180, N.182, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain 3, 1 interactions with chain 1 Metal complexes: 3:D.228, 3:D.228, 3:D.231, 3:D.231, 1:D.301 CA.30: 5 residues within 4Å: Chain 1: D.95 Chain 3: G.206, C.207, T.214, E.216 4 PLIP interactions: 1 interactions with chain 1, 3 interactions with chain 3 Metal complexes: 1:D.95, 3:G.206, 3:T.214, 3:E.216 CA.32: 6 residues within 4Å: Chain 2: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:D.151, 2:E.154, 2:E.222, 2:L.224 CA.33: 7 residues within 4Å: Chain 2: Q.177, D.179, E.180, D.228, V.229, D.231 Chain 3: D.301 5 PLIP interactions: 4 interactions with chain 2, 1 interactions with chain 3 Metal complexes: 2:D.228, 2:D.228, 2:D.231, 2:D.231, 3:D.301 CA.34: 5 residues within 4Å: Chain 2: G.206, C.207, T.214, E.216 Chain 3: D.95 4 PLIP interactions: 1 interactions with chain 3, 3 interactions with chain 2 Metal complexes: 3:D.95, 2:G.206, 2:T.214, 2:E.216 CA.36: 5 residues within 4Å: Chain 3: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 3 Metal complexes: 3:D.151, 3:E.154, 3:E.222, 3:L.224 CA.38: 6 residues within 4Å: Chain 4: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:D.151, 4:E.154, 4:E.222, 4:L.224 CA.39: 5 residues within 4Å: Chain 4: Q.177, D.228, V.229, D.231 Chain 5: D.301 5 PLIP interactions: 1 interactions with chain 5, 4 interactions with chain 4 Metal complexes: 5:D.301, 4:D.228, 4:D.228, 4:V.229, 4:D.231 CA.40: 5 residues within 4Å: Chain 4: G.206, C.207, T.214, E.216 Chain 5: D.95 3 PLIP interactions: 1 interactions with chain 5, 2 interactions with chain 4 Metal complexes: 5:D.95, 4:G.206, 4:T.214 CA.41: 8 residues within 4Å: Chain 4: D.301 Chain 6: Q.177, D.179, E.180, N.182, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain 6, 1 interactions with chain 4 Metal complexes: 6:D.228, 6:D.228, 6:D.231, 6:D.231, 4:D.301 CA.42: 5 residues within 4Å: Chain 4: D.95 Chain 6: G.206, C.207, T.214, E.216 3 PLIP interactions: 1 interactions with chain 4, 2 interactions with chain 6 Metal complexes: 4:D.95, 6:G.206, 6:T.214 CA.44: 4 residues within 4Å: Chain 5: D.151, E.154, E.222, L.224 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:D.151, 5:E.154, 5:E.222, 5:L.224 CA.45: 6 residues within 4Å: Chain 5: Q.177, N.182, D.228, V.229, D.231 Chain 6: D.301 5 PLIP interactions: 1 interactions with chain 6, 4 interactions with chain 5 Metal complexes: 6:D.301, 5:D.228, 5:D.228, 5:V.229, 5:D.231 CA.46: 5 residues within 4Å: Chain 5: G.206, C.207, T.214, E.216 Chain 6: D.95 3 PLIP interactions: 2 interactions with chain 5, 1 interactions with chain 6 Metal complexes: 5:G.206, 5:T.214, 6:D.95 CA.48: 5 residues within 4Å: Chain 6: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:D.151, 6:E.154, 6:E.222, 6:L.224 CA.50: 6 residues within 4Å: Chain 7: L.150, D.151, E.154, E.222, L.224, V.225 5 PLIP interactions: 5 interactions with chain 7 Metal complexes: 7:D.151, 7:D.151, 7:E.154, 7:E.222, 7:L.224 CA.51: 8 residues within 4Å: Chain 7: Q.177, D.179, E.180, K.183, D.228, V.229, D.231 Chain 8: D.301 5 PLIP interactions: 4 interactions with chain 7, 1 interactions with chain 8 Metal complexes: 7:D.228, 7:D.228, 7:D.231, 7:D.231, 8:D.301 CA.52: 5 residues within 4Å: Chain 7: G.206, C.207, T.214, E.216 Chain 8: D.95 3 PLIP interactions: 2 interactions with chain 7, 1 interactions with chain 8 Metal complexes: 7:G.206, 7:T.214, 8:D.95 CA.53: 7 residues within 4Å: Chain 7: D.301 Chain 9: Q.177, D.179, E.180, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain 9, 1 interactions with chain 7 Metal complexes: 9:D.228, 9:D.231, 9:D.231, 7:D.301 CA.54: 5 residues within 4Å: Chain 7: D.95 Chain 9: G.206, C.207, T.214, E.216 3 PLIP interactions: 2 interactions with chain 9, 1 interactions with chain 7 Metal complexes: 9:G.206, 9:T.214, 7:D.95 CA.56: 6 residues within 4Å: Chain 8: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:D.151, 8:E.154, 8:E.222, 8:L.224 CA.57: 6 residues within 4Å: Chain 8: Q.177, E.180, D.228, V.229, D.231 Chain 9: D.301 5 PLIP interactions: 1 interactions with chain 9, 4 interactions with chain 8 Metal complexes: 9:D.301, 8:D.228, 8:D.228, 8:V.229, 8:D.231 CA.58: 5 residues within 4Å: Chain 8: G.206, C.207, T.214, E.216 Chain 9: D.95 3 PLIP interactions: 1 interactions with chain 9, 2 interactions with chain 8 Metal complexes: 9:D.95, 8:G.206, 8:T.214 CA.60: 6 residues within 4Å: Chain 9: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 9 Metal complexes: 9:D.151, 9:E.154, 9:E.222, 9:L.224 CA.62: 7 residues within 4Å: Chain a: L.150, D.151, E.154, E.222, L.224, V.225 Chain b: K.290 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:D.151, a:E.154, a:E.222, a:L.224 CA.63: 8 residues within 4Å: Chain a: Q.177, D.179, E.180, K.183, D.228, V.229, D.231 Chain b: D.301 4 PLIP interactions: 3 interactions with chain a, 1 interactions with chain b Metal complexes: a:D.228, a:D.228, a:D.231, b:D.301 CA.64: 5 residues within 4Å: Chain a: G.206, C.207, T.214, E.216 Chain b: D.95 3 PLIP interactions: 2 interactions with chain a, 1 interactions with chain b Metal complexes: a:G.206, a:T.214, b:D.95 CA.65: 7 residues within 4Å: Chain a: D.301 Chain c: Q.177, E.180, K.183, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain c, 1 interactions with chain a Metal complexes: c:D.228, c:D.228, c:D.231, c:D.231, a:D.301 CA.66: 5 residues within 4Å: Chain a: D.95 Chain c: G.206, C.207, T.214, E.216 3 PLIP interactions: 1 interactions with chain a, 2 interactions with chain c Metal complexes: a:D.95, c:G.206, c:T.214 CA.68: 5 residues within 4Å: Chain b: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain b Metal complexes: b:D.151, b:E.154, b:E.222, b:L.224 CA.69: 7 residues within 4Å: Chain b: Q.177, D.179, E.180, D.228, V.229, D.231 Chain c: D.301 5 PLIP interactions: 1 interactions with chain c, 4 interactions with chain b Metal complexes: c:D.301, b:D.228, b:D.228, b:D.231, b:D.231 CA.70: 5 residues within 4Å: Chain b: G.206, C.207, T.214, E.216 Chain c: D.95 3 PLIP interactions: 1 interactions with chain c, 2 interactions with chain b Metal complexes: c:D.95, b:G.206, b:T.214 CA.72: 5 residues within 4Å: Chain c: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain c Metal complexes: c:D.151, c:E.154, c:E.222, c:L.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herrmann, T. et al., Functional refolding of the penetration protein on a non-enveloped virus. Nature (2021)

Release Date

2021-01-20

Peptides

Outer capsid protein VP4: ABC
Intermediate capsid protein VP6: DEFGHIJKLMNOPQRSTU
Outer capsid glycoprotein VP7: VWXYZ0123456789abc

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
A

E
B

F
C

G
D

H
E

I
F

J
G

K
H

L
I

M
J

N
K

O
L

P
M

Q
N

R
O

S
P

T
Q

U
R

V
a

W
b

X
c

Y
d

Z
e

0
f

1
g

2
h

3
i

4
j

5
k

6
l

7
m

8
n

9
o

a
p

b
q

c
r

Outer capsid protein VP4

Intermediate capsid protein VP6

Outer capsid glycoprotein VP7

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