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- PDB-8p0y: The crystal structure of the C-terminal domain of Mengla nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 8p0y
TitleThe crystal structure of the C-terminal domain of Mengla nucleoprotein
Components
  • (C-terminal domain of Mengla nucleoprotein) x 3
  • Nucleoprotein
KeywordsVIRAL PROTEIN / Nucleoprotein / Filovirus / Mengla
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / viral nucleocapsid / Nucleoprotein
Function and homology information
Biological speciesMengla dianlovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.12 Å
AuthorsFerrero, D.S. / Tomas Gilabert, O. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117976GB-I00 Spain
CitationJournal: Microbiol Spectr / Year: 2023
Title: Structural insights on the nucleoprotein C-terminal domain of Mengla virus.
Authors: Ferrero, D.S. / Tomas Gilabert, O. / Verdaguer, N.
History
DepositionMay 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: Nucleoprotein
Z: Nucleoprotein
Y: Nucleoprotein
T: Nucleoprotein
P: Nucleoprotein
S: Nucleoprotein
X: Nucleoprotein
W: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein
U: Nucleoprotein
a: Nucleoprotein
O: Nucleoprotein
A: Nucleoprotein
C: C-terminal domain of Mengla nucleoprotein
B: C-terminal domain of Mengla nucleoprotein
D: C-terminal domain of Mengla nucleoprotein


Theoretical massNumber of molelcules
Total (without water)206,06717
Polymers206,06717
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15230 Å2
ΔGint-63 kcal/mol
Surface area53510 Å2
Unit cell
Length a, b, c (Å)177.182, 177.182, 90.953
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
Nucleoprotein / / Nucleocapsid protein


Mass: 14277.541 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q1NMU1
#2: Protein/peptide C-terminal domain of Mengla nucleoprotein


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Production host: Escherichia coli (E. coli)
#3: Protein/peptide C-terminal domain of Mengla nucleoprotein


Mass: 2826.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Production host: Escherichia coli (E. coli)
#4: Protein/peptide C-terminal domain of Mengla nucleoprotein


Mass: 2911.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Production host: Escherichia coli (E. coli)

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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: 3.92 Å3/Da / Density % sol: 68.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaCl, 0.1M HEPES pH7, 1.6M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.12→48.9 Å / Num. obs: 12572 / % possible obs: 83.8 % / Redundancy: 5 % / Biso Wilson estimate: 146.91 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.284 / Net I/σ(I): 5.4
Reflection shellResolution: 4.12→4.5 Å / Rmerge(I) obs: 1.821 / Num. unique obs: 660 / CC1/2: 0.449

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Processing

Software
NameVersionClassification
REFMACdev_4788refinement
PHENIXdev_4788refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.12→48.9 Å / SU ML: 0.6136 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.9244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 672 5.36 %
Rwork0.2362 11874 -
obs0.238 12546 51.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 176.47 Å2
Refinement stepCycle: LAST / Resolution: 4.12→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8000 0 0 0 8000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058204
X-RAY DIFFRACTIONf_angle_d0.822111177
X-RAY DIFFRACTIONf_chiral_restr0.04451212
X-RAY DIFFRACTIONf_plane_restr0.00681489
X-RAY DIFFRACTIONf_dihedral_angle_d11.3523066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.12-4.440.3232260.3246478X-RAY DIFFRACTION10.25
4.44-4.890.3857830.30551341X-RAY DIFFRACTION29.07
4.89-5.590.33291030.32362271X-RAY DIFFRACTION48.31
5.6-7.050.36311960.29973278X-RAY DIFFRACTION70.81
7.05-48.90.20892640.18724506X-RAY DIFFRACTION97.01
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)
10.2639864416520.3313968268740.3557055743980.725659866547-0.03091205363791.1307090564-0.9054674927220.567506379686-0.373337993493-0.1372007954450.0969979197930.6206168845060.1187085153641.2655603313-0.370426742831.401738158590.3592227296060.05522298713661.02984828423-0.1120024682561.66603599107-92.492270142110.30227070618.4950215065
21.960006781342.80924754005-0.8193492224444.57012047757-0.4329835597791.06276974061-0.1957180031140.471901798053-0.884803542061-0.5411803988-0.854646294183-1.114472135570.602485003199-0.998147361465-1.978767087561.229126372050.631519426048-0.09258819404941.23885020668-0.2455560789810.658732742973-115.7894347353.99959261-1.58918347006
31.730648624330.163143902745-2.510595276831.963862280751.552564663845.33665621758-1.226364965910.685169614480.4903393719140.6595750911990.1120209172930.2327689388430.659615224379-0.603246526909-1.512038883520.8503771247130.767327147502-0.2522641251361.343975148170.198337679811.38438404846-110.4382311643.134563759516.4894266493
41.229535480830.0752131075582-0.8828651538340.09306995331690.0326019400840.8385341992160.1804363021110.750213443769-0.2933876817280.380023710583-0.4505069322750.2951750032070.337762747775-0.6277819219710.0004997819564190.9250219238210.0236282291239-0.4486804350550.651203324628-0.09269117937511.0387542335-69.9273420371-7.549835530036.81301490405
51.672062500171.087517284820.8525902114720.9329483826050.7115563893030.9913438529480.2384729632840.976931038517-1.29901844372-0.8001241280470.36486241740.4604897600020.692033893020.7036577103550.1185232742230.9123054837890.535354109528-0.1950031275870.841530926810.3167426154691.15481503637-64.3286200729-60.693838294413.9534831512
62.06420708379-0.599306676562-1.002236978732.54445633042-2.316029168463.75395075108-1.07117535972-0.122828866213-0.5389405734740.0439854292519-0.1137205372220.957639244406-0.3761636680350.877877057052-0.5426493650061.528225087750.245572192902-0.1049835652921.02516144176-0.0517385585940.919232828048-77.4982204829-26.072986535717.750430002
7-0.01284974100330.06250965791010.0007109804077140.1843949637650.1697647792330.1544775721850.200942649910.213123078511-0.6198905127480.262124786137-0.408337183553-0.38385563526-0.3303435444730.8841732614992.07467871525E-51.538450482220.05284307050580.0860846351230.8578920657430.06522209560471.30267240858-114.77977972724.88376133234.99635487463
80.2815658550060.462436119973-0.146380041231.207737789890.2141352044480.346705080660.09205399140210.1517229745870.3976744372520.8750639813070.33826138423-1.370127153791.000119647250.507912309780.04349120324681.247677554080.1886415491370.1166320252190.984982414464-0.1400545160221.20109108197-92.793216044625.35354296291.65482363171
90.1037649495120.134189200770.1008985117260.1162186821490.06863572365550.323764216271-0.6460770642690.173852276176-0.533445950697-0.248757903502-0.103353117836-0.254959157675-0.167590518862-1.296234069171.56023606916E-70.9407298623750.2262536931050.05550864551091.191307958450.01783775326761.28010361329-52.8019785046-41.68425743210.8558273519
100.4161149954620.1165593334180.07103088573813.0101236087-2.016042029531.416107878050.481582967013-0.0844704430640.0686097787370.560407958798-0.781456079749-0.767952607438-0.01076874960510.601892770633-0.635095984111.972230573810.04258540343590.5437862479720.787196457001-0.3664707677230.945999568094-69.7940702542-36.0565482771-1.01406342607
110.1461315530220.00909111998980.05589727265910.149621991137-0.3253653496030.4395416692350.577064402027-0.73930033394-0.3322120305310.182114830606-0.4562717517310.548486586103-0.21277089390.4262235541160.002950885984181.22892849346-0.02032999689770.142982928561.13341777159-0.07263974362430.688684207996-92.7992982272-5.560551403912.87769178063
121.1529042333-0.1466740191840.5553428047430.05213166152560.04448601604820.537977367580.115002495131.253894811690.1477473585330.271339484301-0.589550000173-0.0806783364565-0.548581083408-0.0039735122859-0.03865116655941.122061677430.0979059522107-0.2333391621.00708006993-0.1676154991931.16330677821-135.91857372456.48199321639.53983883691
130.9376375235350.648837677484-0.4614292627530.500937816664-0.1899014579780.2928574870290.7804677812-0.679886991834-0.6980582186630.572709471071-0.583048513643-0.8878585198141.031205715930.8329536664290.01830522087971.595232747520.452840217806-0.1569851341430.877115246260.08933880919041.24613858076-50.7173913375-68.3316851988-2.39324836743
140.4292552911410.519581805054-0.2450787767960.581765009354-0.4324207328220.709526681519-0.878705448573-0.0642098044695-0.747871800465-0.8880581815020.805206325519-0.6892305578790.857636562007-0.614544076342-0.01936988126561.006688336250.3284643876620.02313474821931.01261207195-0.0474994186040.924511945959-37.8121835616-76.299110641113.3217442894
150.180765982247-0.1569807455-0.3625826507150.2369230200390.1999332799940.8700327515340.101421967237-0.3558151855680.02307915692520.0845459263484-0.183640646492-0.0242762990176-0.0291739745152-0.143199636887-0.471606228430.8499013309880.079916424349-0.499489685151.01792325221-0.3504168159350.647354656992-23.2295750497-70.521288536311.4815049686
160.491648029809-0.0197704928737-0.3130103948520.5032887808270.04805087877720.5674665352550.03339604020780.2340032559670.356422065954-0.3806246043790.01014762998680.266718838087-0.328377803155-0.380187300518-0.16342195982-0.2247451908170.564571840485-0.03046297782830.03026719340760.248446126407-0.0511362621098-67.0426205034-65.271434478432.9203975939
170.1125497434510.185772086046-0.1058152883960.444659052726-0.4164787256480.555694549725-0.0151268183623-0.05388412341450.2976735283841.063727402210.715428681145-0.1187374878240.0006127366163040.4064895402960.5618118502591.048872851460.1257301094630.4519294503980.303394392464-0.2980682220340.642355261248-86.832227589626.1547912177-16.2452673397
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'V' and resid 632 through 697)VA632 - 6971 - 66
22(chain 'Z' and resid 634 through 697)ZB634 - 6971 - 64
33(chain 'Y' and resid 633 through 697)YC633 - 6971 - 65
44(chain 'T' and resid 632 through 697)TD632 - 6971 - 66
55(chain 'P' and resid 633 through 697)PE633 - 6971 - 65
66(chain 'S' and resid 634 through 697)SF634 - 6971 - 64
77(chain 'X' and resid 633 through 697)XG633 - 6971 - 65
88(chain 'W' and resid 632 through 697)WH632 - 6971 - 66
99(chain 'Q' and resid 633 through 697)QI633 - 6971 - 65
1010(chain 'R' and resid 635 through 697)RJ635 - 6971 - 63
1111(chain 'U' and resid 629 through 697)UK629 - 6971 - 69
1212(chain 'a' and resid 628 through 697)aL628 - 6971 - 70
1313(chain 'O' and resid 633 through 697)OM633 - 6971 - 65
1414(chain 'A' and resid 632 through 697)AN632 - 6971 - 66
1515(chain 'C' and resid 103 through 107)CO103 - 1071 - 5
1616(chain 'B' and resid 591 through 623)BP591 - 6231 - 33
1717(chain 'D' and resid 590 through 623)DQ590 - 6231 - 32

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