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- PDB-8p24: The crystal structure of the C-terminal domain of Mengla nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 8p24
TitleThe crystal structure of the C-terminal domain of Mengla nucleoprotein
ComponentsNucleoprotein
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: 3.73 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 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
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
E: Nucleoprotein
L: Nucleoprotein
K: Nucleoprotein
H: Nucleoprotein
B: Nucleoprotein
G: Nucleoprotein
C: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
I: Nucleoprotein
D: Nucleoprotein
J: Nucleoprotein
F: Nucleoprotein
b: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)399,77128
Polymers399,77128
Non-polymers00
Water0
1
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


Theoretical massNumber of molelcules
Total (without water)199,88614
Polymers199,88614
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Nucleoprotein
L: Nucleoprotein
K: Nucleoprotein
H: Nucleoprotein
B: Nucleoprotein
G: Nucleoprotein
C: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
I: Nucleoprotein
D: Nucleoprotein
J: Nucleoprotein
F: Nucleoprotein
b: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)199,88614
Polymers199,88614
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.748, 162.942, 175.363
Angle α, β, γ (deg.)90.000, 99.151, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "a" and (resid 638 or resid 640 or resid...
d_2ens_1(chain "b" and (resid 638 or resid 640 or resid...
d_3ens_1(chain "A" and (resid 638 or resid 640 or resid...
d_4ens_1(chain "B" and (resid 638 or resid 640 or resid...
d_5ens_1(chain "C" and (resid 638 or resid 640 or resid...
d_6ens_1(chain "D" and (resid 638 or resid 640 or resid...
d_7ens_1(chain "E" and (resid 638 or resid 640 or resid...
d_8ens_1(chain "F" and (resid 638 or resid 640 or resid...
d_9ens_1(chain "G" and (resid 638 or resid 640 or resid...
d_10ens_1(chain "H" and (resid 638 or resid 640 or resid...
d_11ens_1(chain "I" and (resid 638 or resid 640 or resid...
d_12ens_1(chain "J" and (resid 638 or resid 640 or resid...
d_13ens_1(chain "K" and (resid 638 or resid 640 or resid...
d_14ens_1(chain "L" and (resid 638 or resid 640 or resid...
d_15ens_1(chain "M" and (resid 638 or resid 640 or resid...
d_16ens_1(chain "N" and (resid 638 or resid 640 or resid...
d_17ens_1(chain "O" and (resid 638 or resid 640 or resid...
d_18ens_1(chain "P" and (resid 638 or resid 640 or resid...
d_19ens_1(chain "Q" and (resid 638 or resid 640 or resid...
d_20ens_1(chain "R" and (resid 638 or resid 640 or resid...
d_21ens_1(chain "S" and (resid 638 or resid 640 or resid...
d_22ens_1(chain "T" and (resid 638 or resid 640 or resid...
d_23ens_1(chain "U" and (resid 638 or resid 640 or resid...
d_24ens_1(chain "V" and (resid 638 or resid 640 or resid...
d_25ens_1(chain "W" and (resid 638 or resid 640 or resid...
d_26ens_1(chain "X" and (resid 638 or resid 640 or resid...
d_27ens_1(chain "Y" and (resid 638 or resid 640 or resid...
d_28ens_1(chain "Z" and (resid 638 or resid 640 or resid...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1GLNGLNVA632 - 69765 - 130
d_2ASPASPZB633 - 69766 - 130
d_3ASPASPYC633 - 69766 - 130
d_4TRPTRPTD634 - 69767 - 130
d_5ARGARGPE636 - 69769 - 130
d_6ARGARGSF636 - 69769 - 130
d_7GLNGLNXG632 - 69765 - 130
d_8PROPROWH635 - 69768 - 130
d_9ASPASPQI633 - 69766 - 130
d_10PROPRORJ635 - 69768 - 130
d_11TRPTRPUK634 - 69767 - 130
d_12TRPTRPaL634 - 69767 - 130
d_13ASPASPOM633 - 69766 - 130
d_14GLNGLNAN632 - 69765 - 130
d_15ASPASPEO633 - 69766 - 130
d_16TRPTRPLP634 - 69767 - 130
d_17GLNGLNKQ632 - 69765 - 130
d_18PROPROHR635 - 69768 - 130
d_19TRPTRPBS634 - 69767 - 130
d_20ARGARGGT636 - 69769 - 130
d_21TRPTRPCU634 - 69767 - 130
d_22SERSERMV631 - 69764 - 130
d_23GLNGLNNW632 - 69765 - 130
d_24ASPASPIX633 - 69766 - 130
d_25TRPTRPDY634 - 69767 - 130
d_26GLNGLNJZ632 - 69765 - 130
d_27TRPTRPFAA634 - 69767 - 130
d_28TRPTRPbBA634 - 69767 - 130

NCS oper:
IDCodeMatrixVector
1given(0.856297837092, -0.400914710046, -0.325609289579), (0.406104138872, 0.912161919794, -0.0551367433715), (0.319113526167, -0.0850178060601, 0.943895402081)-3.88783526873, 44.9186778444, -37.8646651343
2given(-0.558820586456, -0.757144393263, 0.338307434005), (0.768580052227, -0.626068916016, -0.131614648566), (0.311455061721, 0.186467370199, 0.931786276127)-2.85406308207, 62.561828277, -166.831540741
3given(0.165209533435, 0.970119883543, -0.177688552297), (-0.939725301558, 0.209526040806, 0.270213241414), (0.299369617151, 0.122336624849, 0.946261899554)-62.2098061629, 66.3147976474, -21.0699627906
4given(-0.905984723614, -0.422857320736, 0.0195797568343), (0.422406181041, -0.906103509909, -0.0234402975464), (0.0276531878085, -0.0129659411839, 0.999533483968)-8.03442312858, 112.908443909, -28.7986724863
5given(0.588976180225, -0.751381156992, -0.297545653714), (0.767547047011, 0.635325757847, -0.0850453528414), (0.252939893555, -0.178290600797, 0.950912126285)4.67077529725, 55.7811554231, 3.37995601827
6given(-0.2142859295, 0.974949745215, -0.0596199188433), (-0.953859046778, -0.19572654223, 0.227692862309), (0.210319897532, 0.105660375597, 0.971906078657)-60.9012831517, 83.3219645298, -58.5422162012
7given(-0.65215791791, -0.757870686859, 0.017946367525), (0.749260493358, -0.647988606178, -0.136819148351), (0.115320263615, -0.075781186733, 0.990433464972)6.5895854156, 105.809426074, -63.9672679181
8given(0.952558869301, -0.00640956567671, -0.304286900775), (-4.48169700804E-5, 0.999775258361, -0.0211997820686), (0.304354396234, 0.0202076776537, 0.952344502403)-17.0895308531, 43.5826172581, -79.6274264672
9given(-0.627677196104, 0.776566854104, -0.0544541880657), (-0.777267384664, -0.62127676298, 0.0993508757822), (0.0433214753665, 0.104685743483, 0.993561344298)-44.2438036751, 106.43173119, -94.6320723905
10given(-0.231017736195, -0.964415886135, -0.128579952304), (0.953606415554, -0.198218092081, -0.226593010011), (0.193043025716, -0.174961671639, 0.965465071186)24.2388142084, 93.6780592219, -96.8724696919
11given(0.832245255136, 0.443613487047, -0.332528058085), (-0.466190808939, 0.884583962252, 0.0133170336905), (0.300056602933, 0.143938486292, 0.942999335737)-25.643877311, 52.8344935464, -121.035712713
12given(-0.917196282304, 0.39837425766, -0.00699503830006), (-0.398326441779, -0.916392475071, 0.0395079411284), (0.0093287462577, 0.0390228454407, 0.999194771817)-23.9005650093, 119.785663351, -129.820922245
13given(0.188075365833, -0.950670219383, -0.246685611145), (0.953278475237, 0.237150481802, -0.18713577325), (0.236406018147, -0.199964454241, 0.950855620809)34.3727461125, 76.26447981, -132.040154424
14given(0.523716739955, 0.786704903323, -0.326827433637), (-0.796969215989, 0.587985042903, 0.138252154012), (0.300933290045, 0.188066436158, 0.934917199827)-28.0148047544, 61.0147524104, -158.682678726
15given(-0.999615350749, -0.0247285362661, 0.0125558767188), (0.0247691632734, -0.999688420004, 0.00309054360127), (0.0124755399393, 0.00340035338648, 0.999916395755)-0.347564491722, 121.731934828, -165.28833772
16given(-0.112406761706, 0.967785858675, 0.22528926222), (-0.96265142076, -0.16226316629, 0.216732339476), (0.246306642281, -0.19251284792, 0.949879908911)-64.0844515571, 41.6161833293, -140.46078306
17given(0.889850463308, -0.456120230993, 0.0109766948632), (0.456195579414, 0.889103009659, -0.037167614092), (0.00719348828612, 0.038081138293, 0.999248758134)-3.79260717895, 2.62084695654, -137.712757023
18given(-0.847162819664, -0.400150076268, 0.349564119215), (0.412474480821, -0.90999767912, -0.0420597987128), (0.334932768852, 0.108554780915, 0.93596789469)-6.61763278918, 73.0054737527, -127.738226242
19given(0.316355903124, 0.942156971423, 0.110721198323), (-0.934050139295, 0.288969728033, 0.20987337507), (0.165738588872, -0.169813831828, 0.971439129683)-52.780124336, 25.9358136123, -105.058747179
20given(0.618124298584, -0.785491735335, 0.0304152136478), (0.782622414858, 0.611319103994, -0.117435551916), (0.0736512543094, 0.0963933961103, 0.992614631126)17.3054273986, 17.1077811423, -102.92121012
21given(-0.949731907531, 0.0468930812664, 0.30953245831), (-0.0410186334894, -0.998833868165, 0.0254632188377), (0.310365551447, 0.0114866329381, 0.950547885032)-14.2127329572, 78.186554236, -87.4000259914
22given(0.672983479441, 0.739458553101, -0.0171547266004), (-0.734659849131, 0.670948055688, 0.10051672818), (0.0858378848405, -0.0550432086162, 0.994787466101)-35.065888929, 17.1659936249, -72.5955343285
23given(0.221135431729, -0.971970610886, 0.079826389168), (0.952920208619, 0.197935912705, -0.229705138095), (0.2074661342, 0.126864124302, 0.969981080808)30.604881845, 38.4832636803, -67.306572617
24given(-0.826557402149, 0.452843086717, 0.334269352119), (-0.459651076789, -0.885829202129, 0.0634626840166), (0.324844191205, -0.101191716405, 0.940338496485)-27.9275748023, 75.3142093526, -45.4669870503
25given(0.899355586826, 0.43659569178, -0.0233180265913), (-0.4366403459, 0.899629690897, 0.00340992510468), (0.0224663476646, 0.00711485600295, 0.99972228246)-20.2525063696, 10.4050334091, -37.6059626649
26given(-0.188710124777, -0.962570888604, 0.194539901355), (0.946017579489, -0.23134346491, -0.227004274279), (0.263513240853, 0.14120016167, 0.954265836253)32.6789368085, 52.6715608907, -30.0101736117
27given(-0.566940042526, 0.764116341397, 0.307742107926), (-0.772017836499, -0.623173931387, 0.125070825406), (0.287345520775, -0.166674737286, 0.94321369988)-34.6280225, 62.6750063662, -5.5423977851

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Components

#1: Protein ...
Nucleoprotein / / Nucleocapsid protein


Mass: 14277.541 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q1NMU1

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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, sitting drop / pH: 6.5 / Details: 0.2M NaCl, 0.1M Cacodylate, 2M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.73→173.13 Å / Num. obs: 8223 / % possible obs: 84.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 108.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Net I/σ(I): 4.7
Reflection shellResolution: 3.73→4.27 Å / Rmerge(I) obs: 0.787 / Num. unique obs: 1356 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
REFMACdev_4788refinement
PHENIXdev_4788refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.73→173.13 Å / SU ML: 0.6382 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.7101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2651 435 5.29 %
Rwork0.2476 7788 -
obs0.2486 8223 25.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.41 Å2
Refinement stepCycle: LAST / Resolution: 3.73→173.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15048 0 0 0 15048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003215453
X-RAY DIFFRACTIONf_angle_d0.668321030
X-RAY DIFFRACTIONf_chiral_restr0.04192252
X-RAY DIFFRACTIONf_plane_restr0.01712792
X-RAY DIFFRACTIONf_dihedral_angle_d12.88635919
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2LX-RAY DIFFRACTIONTorsion NCS0.784923582045
ens_1d_3LX-RAY DIFFRACTIONTorsion NCS0.798719456123
ens_1d_4LX-RAY DIFFRACTIONTorsion NCS0.675923407061
ens_1d_5LX-RAY DIFFRACTIONTorsion NCS0.826630921211
ens_1d_6LX-RAY DIFFRACTIONTorsion NCS0.805857150338
ens_1d_7LX-RAY DIFFRACTIONTorsion NCS0.811078740701
ens_1d_8LX-RAY DIFFRACTIONTorsion NCS0.784054443384
ens_1d_9LX-RAY DIFFRACTIONTorsion NCS0.926715230479
ens_1d_10LX-RAY DIFFRACTIONTorsion NCS0.739483302618
ens_1d_11LX-RAY DIFFRACTIONTorsion NCS0.79792303627
ens_1d_12LX-RAY DIFFRACTIONTorsion NCS0.752296108069
ens_1d_13LX-RAY DIFFRACTIONTorsion NCS0.721092738301
ens_1d_14LX-RAY DIFFRACTIONTorsion NCS0.787725750973
ens_1d_15LX-RAY DIFFRACTIONTorsion NCS0.669272953873
ens_1d_16LX-RAY DIFFRACTIONTorsion NCS0.697262522531
ens_1d_17LX-RAY DIFFRACTIONTorsion NCS0.80462430892
ens_1d_18LX-RAY DIFFRACTIONTorsion NCS0.762027677722
ens_1d_19LX-RAY DIFFRACTIONTorsion NCS0.791512826946
ens_1d_20LX-RAY DIFFRACTIONTorsion NCS0.729053669311
ens_1d_21LX-RAY DIFFRACTIONTorsion NCS0.716949588387
ens_1d_22LX-RAY DIFFRACTIONTorsion NCS0.766151753258
ens_1d_23LX-RAY DIFFRACTIONTorsion NCS0.724298579366
ens_1d_24LX-RAY DIFFRACTIONTorsion NCS0.757800222554
ens_1d_25LX-RAY DIFFRACTIONTorsion NCS0.786122598908
ens_1d_26LX-RAY DIFFRACTIONTorsion NCS0.781601449444
ens_1d_27LX-RAY DIFFRACTIONTorsion NCS0.788957031266
ens_1d_28LX-RAY DIFFRACTIONTorsion NCS0.74210637722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.73-4.270.2862200.369381X-RAY DIFFRACTION3.69
4.27-5.380.3692950.30661415X-RAY DIFFRACTION13.89
5.38-173.130.24793200.23565992X-RAY DIFFRACTION57.21
Refinement TLS params.
IDMethodRefine-ID
1refinedX-RAY DIFFRACTION
2refinedX-RAY DIFFRACTION
3refinedX-RAY DIFFRACTION
4refinedX-RAY DIFFRACTION
5refinedX-RAY DIFFRACTION
6refinedX-RAY DIFFRACTION
7refinedX-RAY DIFFRACTION
8refinedX-RAY DIFFRACTION
9refinedX-RAY DIFFRACTION
10refinedX-RAY DIFFRACTION
11refinedX-RAY DIFFRACTION
12refinedX-RAY DIFFRACTION
13refinedX-RAY DIFFRACTION
14refinedX-RAY DIFFRACTION
15refinedX-RAY DIFFRACTION
16refinedX-RAY DIFFRACTION
17refinedX-RAY DIFFRACTION
18refinedX-RAY DIFFRACTION
19refinedX-RAY DIFFRACTION
20refinedX-RAY DIFFRACTION
21refinedX-RAY DIFFRACTION
22refinedX-RAY DIFFRACTION
23refinedX-RAY DIFFRACTION
24refinedX-RAY DIFFRACTION
25refinedX-RAY DIFFRACTION
26refinedX-RAY DIFFRACTION
27refinedX-RAY DIFFRACTION
28refinedX-RAY DIFFRACTION
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 633 through 697 )
2X-RAY DIFFRACTION2chain 'L' and (resid 634 through 697 )
3X-RAY DIFFRACTION3chain 'K' and (resid 634 through 697 )
4X-RAY DIFFRACTION4chain 'V' and (resid 632 through 697 )
5X-RAY DIFFRACTION5chain 'H' and (resid 635 through 697 )
6X-RAY DIFFRACTION6chain 'Z' and (resid 633 through 697 )
7X-RAY DIFFRACTION7chain 'B' and (resid 634 through 697 )
8X-RAY DIFFRACTION8chain 'Y' and (resid 633 through 697 )
9X-RAY DIFFRACTION9chain 'G' and (resid 632 through 697 )
10X-RAY DIFFRACTION10chain 'C' and (resid 634 through 697 )
11X-RAY DIFFRACTION11chain 'T' and (resid 634 through 697 )
12X-RAY DIFFRACTION12chain 'P' and (resid 636 through 697 )
13X-RAY DIFFRACTION13chain 'M' and (resid 631 through 697 )
14X-RAY DIFFRACTION14chain 'N' and (resid 632 through 697 )
15X-RAY DIFFRACTION15chain 'S' and (resid 636 through 697 )
16X-RAY DIFFRACTION16chain 'I' and (resid 633 through 697 )
17X-RAY DIFFRACTION17chain 'A' and (resid 632 through 697 )
18X-RAY DIFFRACTION18chain 'X' and (resid 632 through 697 )
19X-RAY DIFFRACTION19chain 'W' and (resid 632 through 697 )
20X-RAY DIFFRACTION20chain 'J' and (resid 632 through 697 )
21X-RAY DIFFRACTION21chain 'F' and (resid 634 through 697 )
22X-RAY DIFFRACTION22chain 'Q' and (resid 6333 through 697 )
23X-RAY DIFFRACTION23chain 'R' and (resid 635 through 697 )
24X-RAY DIFFRACTION24chain 'U' and (resid 634 through 697 )
25X-RAY DIFFRACTION25chain 'a' and (resid 634 through 697 )
26X-RAY DIFFRACTION26chain 'b' and (resid 634 through 697 )
27X-RAY DIFFRACTION27chain 'O' and (resid 633 through 697 )
28X-RAY DIFFRACTION28chain 'D' and (resid 634 through 697 )

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