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- PDB-4g1g: Crystal structure of Newcastle disease virus matrix protein -

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Basic information

Entry
Database: PDB / ID: 4g1g
TitleCrystal structure of Newcastle disease virus matrix protein
ComponentsMatrix protein
KeywordsVIRAL PROTEIN / Beta strand / Virus assembly / Membrane / Virus
Function / homology
Function and homology information


viral budding via host ESCRT complex / structural constituent of virion / viral envelope / identical protein binding
Similarity search - Function
Viral matrix protein, N-terminal domain / Viral matrix protein, C-terminal domain / Viral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Viral matrix protein / Topoisomerase I; domain 3 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesNewcastle disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMeng, G. / Rossmann, M.G.
CitationJournal: 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.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Sep 12, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein
B: Matrix protein


Theoretical massNumber of molelcules
Total (without water)79,5982
Polymers79,5982
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-9 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.845, 112.047, 141.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Matrix protein


Mass: 39799.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Newcastle disease virus / Strain: Chicken/Australia-Victoria/32 / Gene: M / Production host: Escherichia coli (E. coli) / References: UniProt: P11206
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, Tris-Cl, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 38782 / Num. obs: 38781 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.883 / SU B: 13.541 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.305 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1920 5 %RANDOM
Rwork0.22 ---
obs0.22 36499 98.92 %-
all-3700 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.848 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å2-0 Å20 Å2
2---0.69 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5213 0 0 208 5421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025305
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.9797186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8055677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60423.459185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.82715955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4181532
X-RAY DIFFRACTIONr_chiral_restr0.1370.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213803
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 131 -
Rwork0.233 2393 -
obs--96.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.7134-0.00941.92352.6072.02219.93380.2405-0.1778-0.35140.03270.17690.68530.003-0.4588-0.41740.1743-0.0302-0.08840.08830.11930.352629.29924.1651108.5629
27.7092-3.02420.82417.6729-1.03636.18350.0891-0.30250.13690.13260.11560.3102-0.4128-0.3695-0.20470.2646-0.06120.05360.21140.00380.115937.903819.9852118.3839
30.76570.02950.47751.2284-0.86311.9860.0673-0.12570.10960.104-0.01840.0246-0.0843-0.0716-0.04890.11040.00670.01570.0715-0.02090.088243.846430.7874112.4461
44.8481-1.22843.53396.5355-4.224111.88080.3581-0.1605-0.09760.5502-0.1794-0.26450.1410.4553-0.17870.1637-0.0421-0.11330.1039-0.00830.111153.230733.4164118.2453
50.39620.14490.15982.0838-1.01242.0645-0.00630.00670.03880.1267-0.0495-0.1127-0.03560.11730.05580.08430.00540.03290.098-0.01020.096743.930828.7429107.962
63.1088-0.3652-0.6471.12050.19092.5659-0.0475-0.0545-0.04760.0583-0.00580.01970.1158-0.09350.05330.1641-0.0313-0.00280.09070.03030.130144.17719.111695.6062
78.1704-2.0321-16.05591.33683.263835.0391-0.57150.4036-0.6052-0.4964-0.2826-0.09881.2051-0.05850.85410.59380.00880.31680.175-0.09070.222156.8494-7.619390.1841
80.6501-0.2528-0.37531.05630.09471.1932-0.0357-0.0291-0.07510.0880.00950.02660.15140.03820.02620.0917-0.01780.00560.07030.00990.094947.14098.1535101.2517
92.57260.5446-0.45361.9078-0.43352.93340.07040.12340.097-0.02880.01830.1725-0.1653-0.1368-0.08870.14350.0407-0.0020.1307-0.0070.148426.613427.791378.1834
103.26170.1576-0.8152.6073-0.85013.89050.19550.0885-0.01780.2586-0.06480.2541-0.1897-0.1273-0.13070.170.0428-0.02260.1966-0.03540.190934.946520.360677.0097
112.7490.553-1.05321.161-1.2212.3821-0.04860.1942-0.289-0.15090.05730.01520.1988-0.3099-0.00870.1096-0.0238-0.00170.0879-0.04030.099331.89919.686373.943
120.5646-0.55630.39781.125-0.74931.27250.05690.0872-0.0545-0.1909-0.06-0.03750.14110.07940.00310.0978-0.01060.00420.1047-0.0090.070840.696717.039277.7138
131.57220.50260.65591.53880.56881.3802-0.0246-0.04140.0043-0.12710.01310.0148-0.01650.01920.01150.16320.02840.0150.08580.01890.135142.125939.443590.5105
145.38653.98763.1246.92774.40475.064-0.3069-0.16290.4512-0.35590.2686-0.3179-0.67860.25760.03820.1437-0.00570.01290.0742-0.03670.200653.348655.388289.972
152.69071.651-0.37422.7644-0.32381.8579-0.07890.11220.1128-0.17070.0454-0.1352-0.15150.17440.03350.12940.00410.03130.0825-0.0110.074645.08638.562683.0512
160.75530.66640.36242.08720.56890.9041-0.15370.09120.1128-0.26860.06080.1425-0.2648-0.03050.0930.11650.00980.02140.08420.0140.119540.186343.139387.4485
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 26
2X-RAY DIFFRACTION2A28 - 55
3X-RAY DIFFRACTION3A56 - 130
4X-RAY DIFFRACTION4A131 - 147
5X-RAY DIFFRACTION5A148 - 185
6X-RAY DIFFRACTION6A186 - 247
7X-RAY DIFFRACTION7A248 - 264
8X-RAY DIFFRACTION8A265 - 363
9X-RAY DIFFRACTION9B8 - 53
10X-RAY DIFFRACTION10B54 - 75
11X-RAY DIFFRACTION11B76 - 108
12X-RAY DIFFRACTION12B109 - 182
13X-RAY DIFFRACTION13B183 - 245
14X-RAY DIFFRACTION14B246 - 271
15X-RAY DIFFRACTION15B272 - 321
16X-RAY DIFFRACTION16B322 - 364

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