SMTL ID : 8bp8.1

SPA of Trypsin untreated Rotavirus TLP spike

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-13-13-2-mer

Ligands

39 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain D: D.151, E.154, E.222, L.224, V.225 Chain F: K.290 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.151, D:E.154, D:E.222, D:L.224 CA.2: 5 residues within 4Å: Chain D: Q.177, D.228, V.229, D.231 Chain F: D.301 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Metal complexes: D:D.228, D:V.229, D:D.231, F:D.301 CA.3: 5 residues within 4Å: Chain D: G.206, C.207, T.214, E.216 Chain F: D.95 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.206, D:T.214, D:E.216 CA.4: 4 residues within 4Å: Chain E: D.151, E.154, E.222, L.224 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.151, E:E.154, E:E.222, E:L.224 CA.5: 6 residues within 4Å: Chain D: D.301 Chain E: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Metal complexes: E:D.228, E:V.229, E:D.231, D:D.301 CA.6: 5 residues within 4Å: Chain D: D.95 Chain E: G.206, C.207, T.214, E.216 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Metal complexes: D:D.95, E:G.206, E:T.214, E:E.216 CA.7: 6 residues within 4Å: Chain E: K.290 Chain F: D.151, E.154, E.222, L.224, V.225 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.154, F:E.222, F:L.224 CA.8: 6 residues within 4Å: Chain E: D.301 Chain F: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Metal complexes: F:D.228, F:V.229, F:D.231, E:D.301 CA.9: 5 residues within 4Å: Chain E: D.95 Chain F: G.206, C.207, T.214, E.216 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Metal complexes: F:G.206, F:T.214, F:E.216, E:D.95 CA.10: 6 residues within 4Å: Chain G: D.151, E.154, E.222, L.224, V.225 Chain I: K.290 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.154, G:E.222, G:L.224 CA.11: 6 residues within 4Å: Chain G: Q.177, K.183, D.228, V.229, D.231 Chain I: D.301 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain I Metal complexes: G:D.228, G:V.229, G:D.231, I:D.301 CA.12: 5 residues within 4Å: Chain G: G.206, C.207, T.214, E.216 Chain I: D.95 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain I Metal complexes: G:G.206, G:T.214, G:E.216, G:E.216, I:D.95 CA.13: 5 residues within 4Å: Chain H: D.151, E.154, E.222, K.223, L.224 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.222, H:L.224 CA.14: 6 residues within 4Å: Chain G: D.301 Chain H: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain H Metal complexes: G:D.301, H:D.228, H:V.229, H:D.231 CA.15: 5 residues within 4Å: Chain G: D.95 Chain H: G.206, C.207, T.214, E.216 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G Metal complexes: H:G.206, H:T.214, H:E.216, G:D.95 CA.16: 5 residues within 4Å: Chain I: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.151, I:E.154, I:E.222, I:L.224 CA.17: 6 residues within 4Å: Chain H: D.301 Chain I: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain H Metal complexes: I:D.228, I:V.229, I:D.231, H:D.301 CA.18: 5 residues within 4Å: Chain H: D.95 Chain I: G.206, C.207, T.214, E.216 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain H Metal complexes: I:G.206, I:T.214, I:E.216, H:D.95 CA.19: 5 residues within 4Å: Chain J: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.151, J:E.154, J:E.222, J:L.224 CA.20: 6 residues within 4Å: Chain J: Q.177, K.183, D.228, V.229, D.231 Chain L: D.301 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain J Metal complexes: L:D.301, J:D.228, J:V.229, J:D.231 CA.21: 4 residues within 4Å: Chain J: G.206, T.214, E.216 Chain L: D.95 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain L Metal complexes: J:G.206, J:T.214, J:E.216, L:D.95 CA.22: 6 residues within 4Å: Chain J: K.290 Chain K: D.151, E.154, E.222, L.224, V.225 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.154, K:E.222, K:L.224 CA.23: 6 residues within 4Å: Chain J: D.301 Chain K: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain J Metal complexes: K:D.228, K:V.229, K:D.231, J:D.301 CA.24: 5 residues within 4Å: Chain J: D.95 Chain K: G.206, C.207, T.214, E.216 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain J Metal complexes: K:G.206, K:T.214, K:E.216, J:D.95 CA.25: 5 residues within 4Å: Chain L: D.151, E.154, E.222, L.224, V.225 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.154, L:E.222, L:L.224 CA.26: 6 residues within 4Å: Chain K: D.301 Chain L: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K Metal complexes: L:D.228, L:V.229, L:D.231, K:D.301 CA.27: 5 residues within 4Å: Chain K: D.95 Chain L: G.206, C.207, T.214, E.216 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain K Metal complexes: L:T.214, L:E.216, K:D.95 CA.28: 5 residues within 4Å: Chain M: D.151, E.154, E.222, L.224 Chain O: K.290 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:D.151, M:E.154, M:E.222, M:L.224 CA.29: 6 residues within 4Å: Chain M: Q.177, K.183, D.228, V.229, D.231 Chain O: D.301 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain O Metal complexes: M:D.228, M:V.229, M:D.231, O:D.301 CA.30: 5 residues within 4Å: Chain M: G.206, C.207, T.214, E.216 Chain O: D.95 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:G.206, M:T.214, M:E.216 CA.31: 5 residues within 4Å: Chain N: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:D.151, N:E.154, N:E.222, N:L.224 CA.32: 6 residues within 4Å: Chain M: D.301 Chain N: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain M Metal complexes: N:D.228, N:V.229, N:D.231, M:D.301 CA.33: 5 residues within 4Å: Chain M: D.95 Chain N: G.206, C.207, T.214, E.216 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain M Metal complexes: N:G.206, N:T.214, N:E.216, M:D.95 CA.34: 5 residues within 4Å: Chain O: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:D.151, O:E.154, O:E.222, O:L.224 CA.35: 6 residues within 4Å: Chain N: D.301 Chain O: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain O Metal complexes: N:D.301, O:D.228, O:V.229, O:D.231 CA.36: 5 residues within 4Å: Chain N: D.95 Chain O: G.206, C.207, T.214, E.216 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain O Metal complexes: N:D.95, O:G.206, O:T.214, O:E.216 CA.37: 4 residues within 4Å: Chain P: D.151, E.154, E.222, L.224 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:D.151, P:E.154, P:E.222, P:L.224 CA.38: 5 residues within 4Å: Chain P: Q.177, K.183, D.228, V.229, D.231 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:D.228, P:V.229, P:D.231 CA.39: 4 residues within 4Å: Chain P: G.206, C.207, T.214, E.216 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:G.206, P:T.214, P:E.216

5 x ZN: ZINC ION(Non-covalent)

ZN.40: 6 residues within 4Å: Chain Q: H.153, K.154 Chain R: H.153, K.154 Chain S: H.153, K.154 3 PLIP interactions: 1 interactions with chain S, 1 interactions with chain Q, 1 interactions with chain R Metal complexes: S:H.153, Q:H.153, R:H.153 ZN.41: 6 residues within 4Å: Chain T: H.153, K.154 Chain U: H.153, K.154 Chain V: H.153, K.154 3 PLIP interactions: 1 interactions with chain V, 1 interactions with chain U, 1 interactions with chain T Metal complexes: V:H.153, U:H.153, T:H.153 ZN.42: 6 residues within 4Å: Chain W: H.153, K.154 Chain X: H.153, K.154 Chain Y: H.153, K.154 3 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain W, 1 interactions with chain X Metal complexes: Y:H.153, W:H.153, X:H.153 ZN.43: 5 residues within 4Å: Chain 0: H.153, K.154 Chain 1: H.153 Chain Z: H.153, K.154 3 PLIP interactions: 1 interactions with chain 0, 1 interactions with chain Z, 1 interactions with chain 1 Metal complexes: 0:H.153, Z:H.153, 1:H.153 ZN.44: 1 residues within 4Å: Chain 2: H.153 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:H.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shah, P.N.M. et al., Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography. Cell Host Microbe (2023)

Release Date

2023-04-05

Peptides

Outer capsid protein VP4: ABC
Outer capsid glycoprotein VP7: DEFGHIJKLMNOP
Intermediate capsid protein VP6: QRSTUVWXYZ012
Inner capsid protein VP2: 34

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
d

R
e

S
f

T
g

U
h

V
i

W
j

X
k

Y
l

Z
m

0
n

1
o

2
p

3
q

4
r

Outer capsid protein VP4

Outer capsid glycoprotein VP7

Intermediate capsid protein VP6

Inner capsid protein VP2

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