SMTL ID : 8uk3.1

The rotavirus VP5*/VP8* conformational transition permeabilizes membranes to Ca2+ (class 6 reconstruction)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-18-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain B: N.69 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain D: N.69 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain F: N.69 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain G: N.69 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain H: N.69 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain I: N.69 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain J: N.69 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain K: N.69 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain L: N.69 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain M: N.69 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain N: N.69 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain O: N.69 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain P: N.69 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain Q: N.69 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain R: N.69 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain S: N.69 Ligand excluded by PLIP NAG.68: 1 residues within 4Å: Chain T: N.69 Ligand excluded by PLIP NAG.69: 1 residues within 4Å: Chain U: N.69 Ligand excluded by PLIP

54 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain B: L.150, 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.3: 6 residues within 4Å: Chain B: Q.177, E.180, D.228, V.229, D.231 Chain T: D.301 4 PLIP interactions: 1 interactions with chain T, 3 interactions with chain B Metal complexes: T:D.301, B:D.228, B:D.228, B:D.231 CA.4: 5 residues within 4Å: Chain B: G.206, C.207, T.214, E.216 Chain T: D.95 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain T Metal complexes: B:G.206, B:T.214, T:D.95 CA.6: 6 residues within 4Å: Chain D: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.151, D:E.154, D:E.222, D:L.224 CA.7: 5 residues within 4Å: Chain D: Q.177, D.228, V.229, D.231 Chain F: D.301 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Metal complexes: D:D.228, D:D.228, D:V.229, D:D.231, F:D.301 CA.8: 5 residues within 4Å: Chain D: G.206, C.207, T.214, E.216 Chain F: D.95 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Metal complexes: F:D.95, D:G.206, D:T.214 CA.10: 6 residues within 4Å: Chain F: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.151, F:E.154, F:E.222, F:L.224 CA.11: 7 residues within 4Å: Chain F: Q.177, D.179, E.180, D.228, V.229, D.231 Chain G: D.301 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain G Metal complexes: F:D.228, F:D.228, F:D.231, F:D.231, G:D.301 CA.12: 5 residues within 4Å: Chain F: G.206, C.207, T.214, E.216 Chain G: D.95 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Metal complexes: F:G.206, F:T.214, F:E.216, G:D.95 CA.13: 8 residues within 4Å: Chain D: D.301 Chain G: Q.177, D.179, E.180, N.182, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain D Metal complexes: G:D.228, G:D.228, G:D.231, G:D.231, D:D.301 CA.14: 5 residues within 4Å: Chain D: D.95 Chain G: G.206, C.207, T.214, E.216 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain D Metal complexes: G:G.206, G:T.214, G:E.216, D:D.95 CA.16: 5 residues within 4Å: Chain G: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.151, G:E.154, G:E.222, G:L.224 CA.17: 5 residues within 4Å: Chain H: G.206, C.207, T.214, E.216 Chain I: D.95 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain I Metal complexes: H:G.206, H:T.214, I:D.95 CA.19: 6 residues within 4Å: Chain H: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.151, H:E.154, H:E.222, H:L.224 CA.20: 5 residues within 4Å: Chain H: Q.177, D.228, V.229, D.231 Chain I: D.301 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain I Metal complexes: H:D.228, H:D.228, H:V.229, H:D.231, I:D.301 CA.22: 4 residues within 4Å: Chain I: D.151, E.154, E.222, L.224 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.151, I:E.154, I:E.222, I:L.224 CA.23: 6 residues within 4Å: Chain I: Q.177, N.182, D.228, V.229, D.231 Chain J: D.301 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain J Metal complexes: I:D.228, I:D.228, I:V.229, I:D.231, J:D.301 CA.24: 5 residues within 4Å: Chain I: G.206, C.207, T.214, E.216 Chain J: D.95 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Metal complexes: I:G.206, I:T.214, J:D.95 CA.25: 8 residues within 4Å: Chain H: D.301 Chain J: Q.177, D.179, E.180, N.182, D.228, V.229, D.231 5 PLIP interactions: 1 interactions with chain H, 4 interactions with chain J Metal complexes: H:D.301, J:D.228, J:D.228, J:D.231, J:D.231 CA.26: 5 residues within 4Å: Chain H: D.95 Chain J: G.206, C.207, T.214, E.216 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain H Metal complexes: J:G.206, J:T.214, H:D.95 CA.28: 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.30: 6 residues within 4Å: Chain K: L.150, D.151, E.154, E.222, L.224, V.225 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:D.151, K:D.151, K:E.154, K:E.222, K:L.224 CA.31: 8 residues within 4Å: Chain K: Q.177, D.179, E.180, K.183, D.228, V.229, D.231 Chain L: D.301 5 PLIP interactions: 1 interactions with chain L, 4 interactions with chain K Metal complexes: L:D.301, K:D.228, K:D.228, K:D.231, K:D.231 CA.32: 5 residues within 4Å: Chain K: G.206, C.207, T.214, E.216 Chain L: D.95 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain L Metal complexes: K:G.206, K:T.214, L:D.95 CA.34: 6 residues within 4Å: Chain L: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.151, L:E.154, L:E.222, L:L.224 CA.35: 6 residues within 4Å: Chain L: Q.177, E.180, D.228, V.229, D.231 Chain M: D.301 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain M Metal complexes: L:D.228, L:D.228, L:V.229, L:D.231, M:D.301 CA.36: 5 residues within 4Å: Chain L: G.206, C.207, T.214, E.216 Chain M: D.95 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain M Metal complexes: L:G.206, L:T.214, M:D.95 CA.37: 7 residues within 4Å: Chain K: D.301 Chain M: Q.177, D.179, E.180, D.228, V.229, D.231 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain M Metal complexes: K:D.301, M:D.228, M:D.231, M:D.231 CA.38: 5 residues within 4Å: Chain K: D.95 Chain M: G.206, C.207, T.214, E.216 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain K Metal complexes: M:G.206, M:T.214, K:D.95 CA.40: 6 residues within 4Å: Chain M: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:D.151, M:E.154, M:E.222, M:L.224 CA.42: 7 residues within 4Å: Chain N: L.150, D.151, E.154, E.222, L.224, V.225 Chain O: K.290 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:D.151, N:E.154, N:E.222, N:L.224 CA.43: 8 residues within 4Å: Chain N: Q.177, D.179, E.180, K.183, D.228, V.229, D.231 Chain O: D.301 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain O Metal complexes: N:D.228, N:D.228, N:D.231, O:D.301 CA.44: 5 residues within 4Å: Chain N: G.206, C.207, T.214, E.216 Chain O: D.95 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O Metal complexes: N:G.206, N:T.214, O:D.95 CA.46: 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.47: 7 residues within 4Å: Chain O: Q.177, D.179, E.180, D.228, V.229, D.231 Chain P: D.301 5 PLIP interactions: 4 interactions with chain O, 1 interactions with chain P Metal complexes: O:D.228, O:D.228, O:D.231, O:D.231, P:D.301 CA.48: 5 residues within 4Å: Chain O: G.206, C.207, T.214, E.216 Chain P: D.95 3 PLIP interactions: 1 interactions with chain P, 2 interactions with chain O Metal complexes: P:D.95, O:G.206, O:T.214 CA.49: 5 residues within 4Å: Chain N: D.95 Chain P: G.206, C.207, T.214, E.216 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain P Metal complexes: N:D.95, P:G.206, P:T.214 CA.50: 7 residues within 4Å: Chain N: D.301 Chain P: Q.177, E.180, K.183, D.228, V.229, D.231 5 PLIP interactions: 1 interactions with chain N, 4 interactions with chain P Metal complexes: N:D.301, P:D.228, P:D.228, P:D.231, P:D.231 CA.52: 5 residues within 4Å: Chain P: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:D.151, P:E.154, P:E.222, P:L.224 CA.54: 6 residues within 4Å: Chain Q: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:D.151, Q:E.154, Q:E.222, Q:L.224 CA.55: 8 residues within 4Å: Chain Q: Q.177, D.179, E.180, K.183, D.228, V.229, D.231 Chain R: D.301 5 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain R Metal complexes: Q:D.228, Q:D.228, Q:D.231, Q:D.231, R:D.301 CA.56: 5 residues within 4Å: Chain Q: G.206, C.207, T.214, E.216 Chain R: D.95 3 PLIP interactions: 1 interactions with chain R, 2 interactions with chain Q Metal complexes: R:D.95, Q:G.206, Q:T.214 CA.58: 6 residues within 4Å: Chain R: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:D.151, R:E.154, R:E.222, R:L.224 CA.59: 8 residues within 4Å: Chain R: Q.177, E.180, N.182, K.183, D.228, V.229, D.231 Chain S: D.301 4 PLIP interactions: 1 interactions with chain S, 3 interactions with chain R Metal complexes: S:D.301, R:D.228, R:D.228, R:D.231 CA.60: 5 residues within 4Å: Chain R: G.206, C.207, T.214, E.216 Chain S: D.95 3 PLIP interactions: 1 interactions with chain S, 2 interactions with chain R Metal complexes: S:D.95, R:G.206, R:T.214 CA.61: 7 residues within 4Å: Chain Q: D.301 Chain S: Q.177, E.180, K.183, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain S, 1 interactions with chain Q Metal complexes: S:D.228, S:D.228, S:D.231, S:D.231, Q:D.301 CA.62: 5 residues within 4Å: Chain Q: D.95 Chain S: G.206, C.207, T.214, E.216 3 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain S Metal complexes: Q:D.95, S:G.206, S:T.214 CA.64: 6 residues within 4Å: Chain S: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:D.151, S:E.154, S:E.222, S:L.224 CA.65: 6 residues within 4Å: Chain T: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:D.151, T:E.154, T:E.222, T:L.224 CA.66: 5 residues within 4Å: Chain T: Q.177, D.228, V.229, D.231 Chain U: D.301 5 PLIP interactions: 4 interactions with chain T, 1 interactions with chain U Metal complexes: T:D.228, T:D.228, T:V.229, T:D.231, U:D.301 CA.67: 5 residues within 4Å: Chain T: G.206, C.207, T.214, E.216 Chain U: D.95 3 PLIP interactions: 1 interactions with chain U, 2 interactions with chain T Metal complexes: U:D.95, T:G.206, T:T.214 CA.70: 6 residues within 4Å: Chain U: L.150, D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:D.151, U:E.154, U:E.222, U:L.224 CA.71: 7 residues within 4Å: Chain B: D.301, Y.302 Chain U: Q.177, E.180, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain U, 1 interactions with chain B Metal complexes: U:D.228, U:D.228, U:V.229, U:D.231, B:D.301 CA.72: 5 residues within 4Å: Chain B: D.95 Chain U: G.206, C.207, T.214, E.216 3 PLIP interactions: 2 interactions with chain U, 1 interactions with chain B Metal complexes: U:G.206, U:T.214, B:D.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Sautu, M. et al., The rotavirus VP5*/VP8* conformational transition permeabilizes membranes to Ca2. Plos Pathog. (2024)

Release Date

2024-03-27

Peptides

Outer capsid protein VP4: ACE
Outer capsid glycoprotein VP7: BDFGHIJKLMNOPQRSTU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

C
2

E
3

B
f

D
g

F
h

G
i

H
j

I
k

J
l

K
m

L
n

M
o

N
p

O
q

P
r

Q
a

R
b

S
c

T
d

U
e

Outer capsid protein VP4

Outer capsid glycoprotein VP7

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