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- PDB-7skt: Crystal structure of Nipah virus matrix protein -

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Basic information

Entry
Database: PDB / ID: 7skt
TitleCrystal structure of Nipah virus matrix protein
ComponentsMatrix proteinViral matrix protein
KeywordsVIRAL PROTEIN / Matrix / Dimer / Viral assembly
Function / homology
Function and homology information


virion assembly / virion component / host cell cytoplasm / structural constituent of virion / host cell nucleus / host cell plasma membrane / membrane
Similarity search - Function
Viral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Viral matrix protein
Similarity search - Domain/homology
Biological speciesNipah henipavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.048 Å
AuthorsNorris, M.J. / Saphire, E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Sci Adv / Year: 2022
Title: Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerization.
Authors: Norris, M.J. / Husby, M.L. / Kiosses, W.B. / Yin, J. / Saxena, R. / Rennick, L.J. / Heiner, A. / Harkins, S.S. / Pokhrel, R. / Schendel, S.L. / Hastie, K.M. / Landeras-Bueno, S. / Salie, Z.L. ...Authors: Norris, M.J. / Husby, M.L. / Kiosses, W.B. / Yin, J. / Saxena, R. / Rennick, L.J. / Heiner, A. / Harkins, S.S. / Pokhrel, R. / Schendel, S.L. / Hastie, K.M. / Landeras-Bueno, S. / Salie, Z.L. / Lee, B. / Chapagain, P.P. / Maisner, A. / Duprex, W.P. / Stahelin, R.V. / Saphire, E.O.
History
DepositionOct 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein
B: Matrix protein


Theoretical massNumber of molelcules
Total (without water)87,9232
Polymers87,9232
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, 84.89 kDa by SEC-MALS, electron microscopy, dimer in solution by single particle analysis of negative stain TEM, microscopy, bimolecular fluorescence complementation (BiFC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-15 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.445, 78.453, 135.38
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Matrix protein / Viral matrix protein / Protein M


Mass: 43961.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah henipavirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IK90
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M TRIS pH 7.5, 20% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.048→67.879 Å / Num. obs: 40796 / % possible obs: 98.7 % / Redundancy: 5.42 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.225 / Rmerge(I) obs: 0.0728 / Rpim(I) all: 0.034 / Rrim(I) all: 0.0806 / AbsDiff over sigma anomalous: 0.693 / Net I/σ(I): 13.91 / Num. measured all: 221300 / % possible anomalous: 98.5 / Redundancy anomalous: 2.85
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
5.557-67.8794.910.024741.161073010730218721871-0.3380.01190.02750.6397.82.7597.4
4.411-5.5575.310.027641.71121611216211221121-0.3940.01280.03050.60799.12.8699.2
3.854-4.4114.830.031135.0798069806203220320.999-0.3530.01540.03490.6796.32.5796.3
3.501-3.8545.10.041629.991058310583207720770.999-0.320.02010.04640.74199.12.799.3
3.25-3.5015.340.051424.551098710987205620560.999-0.2090.02410.05690.70799.52.8199.1
3.059-3.255.560.079219.261148611486206420640.998-0.1360.03610.08730.72699.22.9399.5
2.906-3.0595.760.107714.851169211692202920290.997-0.1290.04840.11830.69399.63.0299.7
2.779-2.9065.20.173210.571045710457201120110.993-0.1340.08250.19270.73696.32.7496.3
2.672-2.7795.270.22048.841067010670202520250.991-0.0870.10560.24520.73499.52.7599.6
2.58-2.6725.580.24827.921149311493206020600.987-0.0070.11380.27370.799.42.9299.5
2.499-2.585.630.31016.741143411434203020300.98-0.0550.14150.34160.68699.22.9599.7
2.428-2.4995.740.36135.941161011610202320230.971-0.0730.16310.39720.69198.63.0199.2
2.364-2.4285.720.3985.311152411524201320130.971-0.0640.18010.43780.66398.82.9999.1
2.306-2.3645.780.44394.571182911829204520450.973-0.0180.19930.48750.68599.63.0199.9
2.254-2.3065.580.63173.851116211162200120010.94-0.0860.28950.69630.79297.62.9298.6
2.206-2.2545.660.58973.61146011460202520250.938-0.0560.26840.64960.69798.42.9598.7
2.162-2.2065.120.86612.5199399939194019400.914-0.050.41820.96580.67495.72.6695.4
2.121-2.1625.330.82662.671075010750201820180.916-0.0340.3930.91770.69199.42.7699.6
2.083-2.1215.51.10942.231103611036200520050.843-0.0440.51521.2260.66198.82.8599
2.048-2.0835.61.04682.31143611436204320430.896-0.0490.48071.15430.6698.72.998.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5 20210420data processing
XDSFeb 5, 2021data reduction
Aimless0.7.7data scaling
TRUNCATE7.1.014data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BK6

6bk6


Resolution: 2.048→29.61 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.436 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 2099 -RANDOM
Rwork0.2141 ---
obs0.2161 40680 98.4 %-
Displacement parametersBiso mean: 54.46 Å2
Baniso -1Baniso -2Baniso -3
1-10.805 Å20 Å20 Å2
2---7.3015 Å20 Å2
3----3.5036 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.048→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 0 204 4597
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088883HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9516005HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2653SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1384HARMONIC5
X-RAY DIFFRACTIONt_it4495HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion596SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6613SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion15.18
LS refinement shellResolution: 2.05→2.06 Å
RfactorNum. reflection% reflection
Rfree0.4161 43 -
Rwork0.3358 --
obs0.3403 814 97.61 %
Refinement TLS params.

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)
12.84560.30030.48670.65011.19834.69550.0029-0.0155-0.157-0.0155-0.0215-0.2653-0.157-0.26530.0186-0.18550.0383-0.00780.08540.02220.0544-10.144323.565521.5604
25.4149-0.9192-0.01361.934-0.64763.80410.18-0.05160.1505-0.0516-0.18490.23240.15050.23240.0049-0.2159-0.00650.00750.0744-0.00950.065919.057812.157213.6582
34.9183-0.4106-0.0880.80970.30691.17010.04390.01670.01980.0167-0.0331-0.10740.0198-0.1074-0.0109-0.16590.00010.02220.09050.05010.008213.941215.219612.5122
42.46060.32050.48170.92510.80244.97310.0338-0.0718-0.2701-0.071800.2163-0.27010.2163-0.0338-0.215-0.0202-0.00290.0677-0.06370.12725.023527.55435.2881
53.6362-0.00350.8134.84221.26070.86770.0291-0.09890.2104-0.0989-0.0294-0.04040.2104-0.04040.0003-0.20970.0338-0.00460.1225-0.00310.0135-3.092125.900548.091
65.36910.3756-0.37451.16160.33762.05630.08140.06650.09860.06650.05960.12070.09860.1207-0.1411-0.15640.0373-0.02670.05150.00130.01610.980125.778947.0177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|43 - 181}A43 - 181
2X-RAY DIFFRACTION2{A|182 - 262}A182 - 262
3X-RAY DIFFRACTION3{A|263 - 351}A263 - 351
4X-RAY DIFFRACTION4{B|44 - 180}B44 - 180
5X-RAY DIFFRACTION5{B|181 - 262}B181 - 262
6X-RAY DIFFRACTION6{B|263 - 351}B263 - 351

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