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- PDB-7sku: Nipah virus matrix protein in complex with PI(4,5)P2 -

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Basic information

Entry
Database: PDB / ID: 7sku
TitleNipah virus matrix protein in complex with PI(4,5)P2
ComponentsMatrix proteinViral matrix protein
KeywordsVIRAL PROTEIN / Matrix / Dimer / Viral assembly / lipid complex
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
Chem-PIO / Matrix protein
Similarity search - Component
Biological speciesNipah virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.117 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

Downloads & links

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Assembly

Deposited unit
A: Matrix protein
B: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8008
Polymers87,9232
Non-polymers1,8776
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-83 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.114, 96.471, 119.972
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 virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IK90
#2: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.117→75.18 Å / Num. obs: 45637 / % possible obs: 96.9 % / Redundancy: 12.71 %
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: 0.998 / CC1/2 anomalous: -0.076 / Rmerge(I) obs: 0.2011 / Rpim(I) all: 0.0579 / Rrim(I) all: 0.2095 / AbsDiff over sigma anomalous: 0.755 / Net I/σ(I): 9.95 / Num. measured all: 579838 / % possible anomalous: 96.8 / Redundancy anomalous: 6.7
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
5.746-75.1811.640.046735.792961929619254425440.999-0.1260.01420.04890.7221006.6799.9
4.561-5.74612.80.064431.883097530975241924190.999-0.1480.01850.06710.7531006.97100
3.985-4.56113.070.067230.993128931289239423940.998-0.2770.0190.06990.7551007100
3.62-3.98511.210.112120.732480624806221322130.996-0.0620.03450.11740.82592.75.9993.3
3.361-3.6212.140.153716.972869028690236423640.995-0.0920.04540.16040.8221006.43100
3.163-3.36112.970.190913.363050930509235323530.993-0.0760.05410.19860.8081006.84100
3.004-3.16313.180.26719.743111231112236123610.99-0.0540.07510.27770.7761006.94100
2.873-3.00413.360.38186.883143331433235323530.981-0.0410.10660.39660.7581007.01100
2.763-2.87313.460.52595.223144631446233623360.966-0.0340.14620.54610.7591007.04100
2.668-2.76312.60.75963.622934629346232923290.963-0.0230.22020.79140.7561006.59100
2.584-2.66812.510.95672.792925629256233823380.908-0.0450.27840.9970.7541006.54100
2.51-2.58412.251.00392.52862828628233723370.9520.0020.29551.04720.7661006.38100
2.444-2.5112.871.11392.252991629916232523250.897-0.020.31791.15910.7461006.7100
2.385-2.44412.941.53241.713023030230233723370.784-0.0110.4371.59440.7511006.75100
2.33-2.38513.191.80071.423038630386230323030.738-0.0290.50821.8720.7241006.86100
2.281-2.3313.252.0911.243103931039234223420.717-0.0370.58832.17330.7241006.88100
2.235-2.28112.412.8110.861308813088105510550.554-0.030.8082.92840.69344.96.545.2
2.193-2.23513.372.69370.953037930379227322730.611-0.0490.75512.79890.7141006.93100
2.154-2.19313.212.78840.93133731337237323730.621-0.0090.78482.89830.7281006.86100
2.117-2.15411.523.30850.722635426354228822880.38-0.0050.99583.46010.7441005.96100

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20210420data processing
XDSFeb 5, 2021data reduction
Aimless0.7.7data scaling
TRUNCATE7.1.014data processing
BUSTER2.10.4refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SKT

7skt


Resolution: 2.117→75.18 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.451 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.232 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.189
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 2299 -RANDOM
Rwork0.231 ---
obs0.2327 45498 96.6 %-
Displacement parametersBiso mean: 53.95 Å2
Baniso -1Baniso -2Baniso -3
1--4.5341 Å20 Å20 Å2
2--9.4924 Å20 Å2
3----4.9583 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.117→75.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 114 315 5093
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089627HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9917383HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2882SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1486HARMONIC5
X-RAY DIFFRACTIONt_it4892HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion653SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6761SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion14.45
LS refinement shellResolution: 2.12→2.13 Å
RfactorNum. reflection% reflection
Rfree0.3974 46 -
Rwork0.4136 --
obs0.4129 910 91.79 %
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)
12.0869-1.0344-0.59131.74320.39750.0795-0.03440.1334-0.23150.13340.0718-0.0118-0.2315-0.0118-0.03740.143-0.0202-0.0158-0.11250.0042-0.04629.248825.115220.8045
22.13661.4217-1.1383.4219-0.61941.98810.0641-0.4773-0.1046-0.4773-0.0433-0.1443-0.1046-0.1443-0.02080.15440.0334-0.0629-0.1004-0.0042-0.0782-1.990620.15918.5684
30.1870.34380.17021.5157-0.01770.503-0.0016-0.1670.0499-0.1670.01060.01140.04990.0114-0.00890.0756-0.01450.0444-0.07710.00610.006119.28868.572716.194
40.5946-0.56761.03061.7952-1.32471.6904-0.0488-0.27660.2645-0.27660.1413-0.20570.2645-0.2057-0.09250.1836-0.0428-0.0111-0.08680.011-0.0491-3.4778-20.201719.5477
50.97120.6578-0.01673.36610.25261.4282-0.0156-0.1330.2095-0.133-0.0010.06680.20950.06680.01660.11730.02980.0575-0.10440.0061-0.042415.0566-16.952617.7793
61.4537-0.00021.0352.87420.49221.6968-0.039-0.458-0.0697-0.458-0.0617-0.0771-0.0697-0.07710.10070.2008-0.0034-0.1121-0.157-0.0205-0.1108-9.2709-2.92262.7292
70.0450.28150.2291.43440.30950.078-0.0226-0.41840.053-0.41840.00870.03510.0530.03510.01380.2321-0.0079-0.0744-0.0651-0.0009-0.0565-3.4036-2.94095.7908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|16 - 73}A16 - 73
2X-RAY DIFFRACTION2{A|74 - 168}A74 - 168
3X-RAY DIFFRACTION3{A|169 - 351}A169 - 351
4X-RAY DIFFRACTION4{B|16 - 61}B16 - 61
5X-RAY DIFFRACTION5{B|62 - 180}B62 - 180
6X-RAY DIFFRACTION6{B|181 - 262}B181 - 262
7X-RAY DIFFRACTION7{B|263 - 352}B263 - 352

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