[English] 日本語
Yorodumi
- PDB-7sks: Crystal structure of measles virus matrix protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sks
TitleCrystal structure of measles virus matrix protein
ComponentsMatrix proteinViral matrix protein
KeywordsVIRAL PROTEIN / Matrix / Dimer / Viral assembly
Function / homologyViral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Viral matrix protein / virion assembly / structural constituent of virion / viral envelope / Matrix protein
Function and homology information
Biological speciesMeasles virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.541 Å
AuthorsNorris, M.J. / Saphire, E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Matrix protein
B: Matrix protein


Theoretical massNumber of molelcules
Total (without water)83,4742
Polymers83,4742
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, 80.57 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 area4590 Å2
ΔGint-7 kcal/mol
Surface area24680 Å2
Unit cell
Length a, b, c (Å)85.954, 85.954, 402.506
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Matrix protein / Viral matrix protein


Mass: 41736.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus / Strain: Ichinose-B95a / Gene: M / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9W850
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 19% (v/v) isopropanol, 19% (w/v) PEG 4000, 5% (v/v) glycerol, 0.095 M sodium citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.541→19.998 Å / Num. obs: 30225 / % possible obs: 100 % / Redundancy: 84.53 %
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: 1 / CC1/2 anomalous: -0.033 / Rmerge(I) obs: 0.1428 / Rpim(I) all: 0.0153 / Rrim(I) all: 0.1437 / AbsDiff over sigma anomalous: 0.662 / Net I/σ(I): 29.31 / Num. measured all: 2554941 / % possible anomalous: 100 / Redundancy anomalous: 46.65
Reflection shell

% possible anomalous: 100 / % possible all: 100

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 anomalousRedundancy anomalous
6.811-19.99880.420.05685.571384891384891722172210.0040.00620.05640.74151.23
5.442-6.81190.980.081772.981450271450271594159410.1180.00860.08220.74953.24
4.765-5.44290.680.08874.71141104141104155615561-0.0090.00930.08860.65552.08
4.334-4.76594.20.096972.27145627145627154615461-0.0970.010.09740.6453.22
4.026-4.33494.570.11360.76145168145168153515351-0.1240.01170.11360.65153.17
3.79-4.02694.20.140448.78142523142523151315130.999-0.1820.01460.14110.66852.35
3.602-3.7996.120.17938.8144468144468150315030.999-0.1140.01840.180.6752.89
3.446-3.60294.820.232829.81142608142608150415040.999-0.1190.02410.23410.65952.41
3.314-3.44698.320.31722.86146993146993149514950.998-0.1090.0320.31870.6853.81
3.2-3.31499.110.472115.97148569148569149914990.997-0.0690.04730.47450.65654.36
3.1-3.296.510.604812.54143995143995149214920.996-0.010.06150.60790.67252.32
3.012-3.195.940.79889.62144489144489150615060.993-0.0240.08140.8030.65252.32
2.933-3.01290.961.07146.73133983133983147314730.985-0.040.11221.07740.63349.44
2.861-2.93386.411.58164.44125547125547145314530.9570.0270.17011.59080.66846.6
2.797-2.86181.931.9593.47122644122644149714970.9450.010.21651.97110.65444.58
2.737-2.79779.532.45682.72116909116909147014700.917-0.0420.27542.47240.62642.97
2.683-2.73774.183.15752108299108299146014600.8820.0070.36683.17910.66239.94
2.632-2.68364.064.15891.49563595635149314930.720.0060.52134.19210.66534.62
2.585-2.63246.335.91090.856731367313145314530.403-0.020.87075.97610.62924.71
2.541-2.58538.026.61620.695555155551146114610.4420.0021.07876.70560.63920.24

-
Processing

Software
NameVersionClassification
autoPROC1.0.5 20210420data processing
XDSFeb 5, 2021data reduction
Aimless0.7.7data scaling
TRUNCATE7.1.015data processing
BUSTER2.10.4refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BK6

6bk6


Resolution: 2.541→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.379 / SU Rfree Blow DPI: 0.255
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1517 -RANDOM
Rwork0.2306 ---
obs0.2319 30205 99.9 %-
Displacement parametersBiso mean: 100.56 Å2
Baniso -1Baniso -2Baniso -3
1--6.0511 Å20 Å20 Å2
2---6.0511 Å20 Å2
3---12.1022 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.541→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 0 140 4479
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078863HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9416067HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2665SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1349HARMONIC5
X-RAY DIFFRACTIONt_it4423HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion584SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6197SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion13.21
LS refinement shellResolution: 2.541→2.56 Å
RfactorNum. reflection% reflection
Rfree0.4178 39 -
Rwork0.3421 --
obs--96.04 %
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)
12.57361.38590.0532.83270.17465.45670.21290.0707-0.01950.0707-0.18130.3225-0.01950.3225-0.0315-0.059-0.04210.0315-0.04660.066-0.0888-21.945727.872326.5752
26.1732-0.32281.06854.6421-0.88868.64070.1790.2614-0.78860.2614-0.0963-0.8059-0.7886-0.8059-0.08280.00460.09010.1846-0.28560.0732-0.0276-26.787248.701112.1193
37.3827-1.99622.84418.7155-1.40658.85450.5537-0.0196-1.6321-0.0196-0.6832-0.2974-1.6321-0.29740.12950.30930.07270.3578-0.19940.11290.1235-22.39458.13127.3782
45.6345-2.99233.05618.2787-5.897210.98650.01090.3636-1.2670.36360.2593-1.0055-1.267-1.0055-0.27020.15310.03010.2267-0.1035-0.05990.001-24.354453.785418.2286
52.05440.8381-0.32845.0882-2.11766.52960.37430.3402-0.76940.3402-0.3461-0.0023-0.7694-0.0023-0.02820.0110.04540.1917-0.20.0476-0.0167-19.494849.37678.1954
62.85221.6624-0.63094.6143-0.35052.8391-0.1453-0.50380.0221-0.50380.1117-0.31680.0221-0.31680.03360.00680.08820.01630.06110.1033-0.1524-23.648635.7678-12.1731
76.3908-0.1461-1.04452.296-0.09754.0917-0.0489-0.38120.4126-0.3812-0.0779-0.12330.4126-0.12330.12680.1027-0.0498-0.0356-0.14930.0203-0.0949-35.276719.62136.7826
87.62152.3771-3.59333.63990.43237.9451-0.5658-0.2741.6617-0.2740.283-0.92511.6617-0.92510.28270.2064-0.0972-0.0509-0.3024-0.0315-0.056-40.061710.64855.0591
9-3.28471.89649.17053.28477.34243.5374-0.1725-0.9061-0.0537-0.90610.4985-0.8848-0.0537-0.8848-0.32590.391-0.1665-0.02890.1077-0.01590.2867-48.339315.1812.5333
103.27941.4937-1.32342.8207-2.59136.0364-0.1682-0.59130.8295-0.59130.0361-0.05290.8295-0.05290.13220.14660.00420.002-0.2029-0.029-0.0659-30.72716.20276.438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|32 - 164}A32 - 164
2X-RAY DIFFRACTION2{A|165 - 197}A165 - 197
3X-RAY DIFFRACTION3{A|213 - 244}A213 - 244
4X-RAY DIFFRACTION4{A|245 - 278}A245 - 278
5X-RAY DIFFRACTION5{A|279 - 335}A279 - 335
6X-RAY DIFFRACTION6{B|32 - 164}B32 - 164
7X-RAY DIFFRACTION7{B|165 - 225}B165 - 225
8X-RAY DIFFRACTION8{B|226 - 262}B226 - 262
9X-RAY DIFFRACTION9{B|263 - 278}B263 - 278
10X-RAY DIFFRACTION10{B|279 - 335}B279 - 335

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more