Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Structure and assembly of a paramyxovirus matrix protein. Authors: Anthony J Battisti / Geng Meng / Dennis C Winkler / Lori W McGinnes / Pavel Plevka / Alasdair C Steven / Trudy G Morrison / Michael G Rossmann / Abstract: Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and ...Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and cryoelectron tomography to show that the matrix protein of Newcastle disease virus, a paramyxovirus and relative of measles virus, forms dimers that assemble into pseudotetrameric arrays that generate the membrane curvature necessary for virus budding. We show that the glycoproteins are anchored in the gaps between the matrix proteins and that the helical nucleocapsids are associated in register with the matrix arrays. About 90% of virions lack matrix arrays, suggesting that, in agreement with previous biological observations, the matrix protein needs to dissociate from the viral membrane during maturation, as is required for fusion and release of the nucleocapsid into the host's cytoplasm. Structure and sequence conservation imply that other paramyxovirus matrix proteins function similarly.
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.906 / SU B: 18.642 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28
1680
5 %
RANDOM
Rwork
0.18
-
-
-
obs
0.19
32197
99.42 %
-
all
-
33386
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 60.442 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.94 Å2
0 Å2
-2.36 Å2
2-
-
3.06 Å2
0 Å2
3-
-
-
-2.28 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5018
0
0
71
5089
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.02
5087
X-RAY DIFFRACTION
r_angle_refined_deg
1.809
1.976
6891
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.68
5
647
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.615
23.22
177
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.839
15
916
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.843
15
32
X-RAY DIFFRACTION
r_chiral_restr
0.124
0.2
836
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
3642
X-RAY DIFFRACTION
r_rigid_bond_restr
5.114
3
5087
X-RAY DIFFRACTION
r_sphericity_free
23.997
5
52
X-RAY DIFFRACTION
r_sphericity_bonded
20.928
5
5024
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.393
119
-
Rwork
0.186
2252
-
obs
-
-
99.92 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.7958
-0.1573
-0.4502
0.0652
0.0221
2.5929
0.1057
0.1302
0.1622
-0.0298
0.0448
0.0451
-0.3631
-0.6623
-0.1505
0.0701
0.0787
0.0048
0.2015
0.0913
0.0936
-30.0916
21.628
15.4524
2
2.03
-0.3249
-0.3062
0.5692
-0.0742
2.774
0.0292
-0.4336
0.0657
0.024
0.102
-0.0448
-0.1061
0.3043
-0.1312
0.0391
-0.0137
-0.0127
0.1175
-0.0319
0.0568
-5.4382
15.0826
27.765
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
13 - 361
2
X-RAY DIFFRACTION
2
B
17 - 363
+
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