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- PDB-4csg: Structural insights into Toscana virus RNA encapsidation -

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Basic information

Entry
Database: PDB / ID: 4csg
TitleStructural insights into Toscana virus RNA encapsidation
Components(NUCLEOPROTEIN) x 2
KeywordsVIRAL PROTEIN / INFECTIOUS
Function / homology
Function and homology information


helical viral capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesTOSCANA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsOlal, D. / Daumke, O.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural Insights Into RNA Encapsidation and Helical Assembly of the Toscana Virus Nucleoprotein.
Authors: Olal, D. / Dick, A. / Woods, V.L. / Liu, T. / Li, S. / Devignot, S. / Weber, F. / Saphire, E.O. / Daumke, O.
History
DepositionMar 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
G: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: NUCLEOPROTEIN
J: NUCLEOPROTEIN
K: NUCLEOPROTEIN
L: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)332,89512
Polymers332,89512
Non-polymers00
Water0
1
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)166,4416
Polymers166,4416
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19240 Å2
ΔGint-143.3 kcal/mol
Surface area62420 Å2
MethodPISA
2
G: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: NUCLEOPROTEIN
J: NUCLEOPROTEIN
K: NUCLEOPROTEIN
L: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)166,4556
Polymers166,4556
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19740 Å2
ΔGint-143.3 kcal/mol
Surface area62300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.484, 104.484, 510.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
NUCLEOPROTEIN / / NUCLEOCAPSID PROTEIN / PROTEIN N / RIBONUCLEOPROTEIN


Mass: 27740.109 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOSCANA VIRUS / Description: SYNTHETIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P21701
#2: Protein NUCLEOPROTEIN / / NUCLEOCAPSID PROTEIN / PROTEIN N / RIBONUCLEOPROTEIN


Mass: 27754.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOSCANA VIRUS / Description: SYNTHETIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P21701

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 5 / Details: 6.5% PEG 3350, 0.1 M SODIUM MALONATE, PH 4.5-5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.32→100 Å / Num. obs: 45886 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 66.78 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 10.7
Reflection shellResolution: 3.32→3.41 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 94.5

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Processing

Software
NameClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
MOLREPphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL BASED ON 3OUO
Resolution: 3.32→34.124 Å / SU ML: 0.47 / σ(F): 2.02 / Phase error: 27.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 2295 5 %
Rwork0.2397 --
obs0.241 45879 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.32→34.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22844 0 0 0 22844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323230
X-RAY DIFFRACTIONf_angle_d0.71331352
X-RAY DIFFRACTIONf_dihedral_angle_d10.458707
X-RAY DIFFRACTIONf_chiral_restr0.0293587
X-RAY DIFFRACTIONf_plane_restr0.0034019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3201-3.39220.36341370.34252604X-RAY DIFFRACTION94
3.3922-3.4710.34451440.31112739X-RAY DIFFRACTION99
3.471-3.55770.33411430.2892709X-RAY DIFFRACTION100
3.5577-3.65380.33041440.28952732X-RAY DIFFRACTION100
3.6538-3.76120.30251450.28612768X-RAY DIFFRACTION100
3.7612-3.88240.3091450.27732740X-RAY DIFFRACTION100
3.8824-4.0210.30531440.25152751X-RAY DIFFRACTION100
4.021-4.18170.25091450.24052748X-RAY DIFFRACTION100
4.1817-4.37170.25811430.2232715X-RAY DIFFRACTION100
4.3717-4.60160.25911440.22182728X-RAY DIFFRACTION100
4.6016-4.88920.25991430.2252730X-RAY DIFFRACTION100
4.8892-5.26540.25691440.23832738X-RAY DIFFRACTION100
5.2654-5.7930.2831460.24342758X-RAY DIFFRACTION100
5.793-6.62590.23841420.23272701X-RAY DIFFRACTION99
6.6259-8.32780.20681420.1982709X-RAY DIFFRACTION98
8.3278-34.12580.2031440.17652714X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0130.01970.0135-0.02240.07450.0029-0.1287-0.0275-0.15440.1123-0.01940.28830.29880.0196-00.45460.02920.02650.45630.02830.957926.436523.6023-19.5642
20.04550.0898-0.0750.13880.06860.0617-0.1488-0.1006-0.43480.15970.12950.1042-0.4379-0.1252-00.2825-0.3339-0.5891-2.2903-3.0742-3.328765.094724.6924-17.9613
30.1673-0.0614-0.10210.0586-0.03810.10690.15670.008-0.03590.1924-0.02990.0498-0.0895-0.353900.3540.0233-0.00530.26090.06310.231252.899922.2677-2.61
4-0.0073-0.0605-0.07790.05190.02150.0942-0.16620.0873-0.2779-0.1049-0.1261-0.10360.04210.0613-00.3584-0.049-0.00750.2523-0.11820.288369.471819.5068-16.321
50.2460.04830.0030.1639-0.02730.0681-0.2786-0.00810.0914-0.02150.0924-0.2395-0.0468-0.158300.3260.0279-0.09260.2634-0.04510.286788.885153.9759-13.5515
60.1170.0787-0.09380.0328-0.07410.0855-0.2896-0.4027-0.0708-0.10530.0676-0.03740.0397-0.2067-00.360.1248-0.15320.3453-0.01770.303782.645342.52251.3599
70.03740.0279-0.05240.0055-0.02320.0130.00830.1188-0.06930.0108-0.0616-0.0719-0.27450.4115-00.4047-0.0037-0.09260.3628-0.04550.500895.577355.3483-11.0228
80.19190.2730.28630.0670.02790.13320.0809-0.24430.0946-0.36290.1244-0.26040.1649-0.262100.235-0.03250.00580.34170.11730.302375.009887.635-8.8576
90.02950.00870.03820.1487-0.05010.0460.3079-0.3161-0.1617-0.4170.2704-0.21210.1741-0.2941-0-0.1472-0.2327-0.70320.560.2048-0.042277.115875.93394.9185
100.0076-0.00020.02510.0516-0.10990.02790.03020.0160.0708-0.1324-0.055-0.0102-0.5403-0.00200.3352-0.00660.03730.4135-0.07010.533575.123895.158-6.861
110.1906-0.19930.04740.2670.00140.04340.0977-0.10670.0036-0.0189-0.1579-0.02770.2370.106200.35330.05510.04310.25910.02810.195236.983694.6654-11.756
120.036-0.05880.0384-0.0012-0.0526-0.0607-0.6226-0.0803-0.42090.4312-0.4978-0.3626-0.20660.17820-1.45560.2259-2.30040.48030.3662-1.145948.794793.52964.1998
130.0901-0.15990.10770.0874-0.05140.01220.07520.0222-0.1322-0.0235-0.21810.0081-0.1743-0.0665-0-0.1537-0.40540.0776-0.1172-0.10.604532.71899.755-9.2161
140.13120.0069-0.04950.08980.0610.0531-0.3829-0.6672-0.1739-0.2717-0.25290.46260.15980.097100.6110.0383-0.2903-0.4139-0.13841.802813.952965.0283-11.2448
150.01330.00780.01890.0059-0.03420.0223-0.07940.02010.14530.1471-0.1312-0.1481-0.13530.2584-00.8058-0.01730.01060.6057-0.04620.913326.018271.6671.0485
160.0036-0.01190.0172-0.0202-0.00840.0005-0.1439-0.14190.06020.0201-0.26140.14420.06260.0127-01.0716-0.0378-0.08440.8548-0.00110.967718.644573.138311.5066
170.07660.0424-0.00490.0435-0.0184-0.02260.20350.1630.2168-0.01530.24650.35780.3752-0.209500.81250.2335-0.08720.8514-0.01320.996911.9652.9176-15.7588
180.03620.0406-0.0030.04140.00650.066-0.12620.27470.3268-0.1774-0.1607-0.0186-0.17570.170400.45890.0235-0.07650.44270.01090.487829.258431.4194-22.2719
190.0089-0.04080.0065-0.00170.08750.0837-0.0116-0.72170.22120.43840.0360.3082-0.019-0.0228-00.8710.00040.05650.8972-0.0390.76222.669434.1941-1.8948
200.02750.060.04910.01890.11960.08750.204-0.0215-0.0170.4269-0.01770.19950.6097-0.101600.38950.02210.08280.3807-0.03210.52918.700639.1279-57.2118
210.13180.05970.04090.10220.05570.1019-0.2742-0.764-1.09430.11020.3650.3407-0.1313-0.161900.2717-0.1584-0.3621-0.6099-1.3219-1.117954.859128.1211-60.3921
220.0792-0.0703-0.08990.08760.05450.0201-0.0311-0.36340.1852-0.07710.02750.2876-0.0901-0.0834-00.346-0.0575-0.00240.376-0.10190.396845.126431.6417-45.2791
230.0151-0.0094-0.04540.0069-0.00510.0725-0.0338-0.0158-0.0529-0.0839-0.0007-0.06420.3112-0.016200.35980.0063-0.06510.3238-0.04040.357156.865321.4756-60.5022
240.1820.1370.03070.1045-0.120.07920.1928-0.39050.317-0.2927-0.2485-0.3675-0.0133-0.177-00.3305-0.02770.08270.5494-0.1060.467988.368947.4365-56.2049
250.12150.0456-0.04580.03590.00890.052-0.0905-0.84880.11440.135-0.47040.1367-0.0132-0.1528-00.32580.04330.14050.7057-0.0837-0.065775.751940.3793-42.6614
260.03330.0005-0.03190.00330.03660.039-0.0447-0.105-0.1135-0.0324-0.009-0.1055-0.10570.237500.42020.0041-0.04880.64280.10090.83294.094446.9008-52.4064
270.38280.0474-0.26370.24830.03540.1570.0271-0.00070.09520.01580.01220.01330.21250.102300.40340.10690.08580.48530.06510.432186.904179.8516-48.5387
280.01930.01770.0281-0.0232-0.05730.2545-0.05950.32520.0339-0.28820.1982-0.1963-0.32570.1605-00.46240.03480.11960.495-0.03310.644478.367198.0618-56.5699
290.09690.02510.04310.14460.02170.0633-0.07950.08640.06170.0133-0.2173-0.21990.2473-0.1998-00.33760.0739-0.01090.3520.04930.268950.0408100.439-51.4754
300.1058-0.15670.04240.0755-0.07820.1074-0.0624-0.1065-0.14630.1210.0667-0.20170.14620.098600.41010.0107-0.07190.28210.0370.339562.071893.7356-38.5078
310.0257-0.053-0.01120.04150.02330.0386-0.16760.1245-0.00390.1743-0.08320.0872-0.4042-0.0035-00.4860.02070.04090.3776-0.05350.595448.8293107.5874-49.0334
320.0633-0.00350.02090.12260.01180.00310.03190.30060.1625-0.1833-0.2310.36630.0160.1667-00.32130.2039-0.20140.2046-0.070.479919.799683.3325-61.2151
330.03650.0177-0.00110.0131-0.02190.01830.2125-0.38690.06110.55170.1518-0.2101-0.04590.074-00.99530.0833-0.120.3559-0.2220.437928.305480.9471-40.9482
340.01350.00040.04110.01740.01770.0293-0.0121-0.17260.360.2426-0.34-0.16490.0139-0.0062-01.0066-0.12150.14650.4026-0.28960.578524.210391.8806-37.809
350.0642-0.02630.04040.0017-0.00110.0389-0.03420.27180.05940.0361-0.22970.055-0.0247-0.058800.45190.17730.23720.2144-0.19871.061413.187782.5377-55.22
360.030.01670.01030.10770.02570.0769-0.03830.41440.09060.3733-0.03820.1322-0.1880.0368-00.29010.0689-0.00640.3785-0.07930.271120.629244.94-63.5403
370.00710.09370.02150.07310.17920.09980.03220.17990.51731.1454-0.20490.11570.54430.1695-00.81820.1750.1899-0.3701-1.196-0.961623.374453.4961-42.8885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 5 THROUGH 36 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 37 THROUGH 147 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 148 THROUGH 250 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 4 THROUGH 36 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 37 THROUGH 147 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 148 THROUGH 251 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 4 THROUGH 36 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 37 THROUGH 163 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 164 THROUGH 250 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 4 THROUGH 36 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 37 THROUGH 147 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 148 THROUGH 252 )
13X-RAY DIFFRACTION13CHAIN E AND (RESID 4 THROUGH 36 )
14X-RAY DIFFRACTION14CHAIN E AND (RESID 37 THROUGH 147 )
15X-RAY DIFFRACTION15CHAIN E AND (RESID 148 THROUGH 216 )
16X-RAY DIFFRACTION16CHAIN E AND (RESID 217 THROUGH 251 )
17X-RAY DIFFRACTION17CHAIN F AND (RESID 4 THROUGH 54 )
18X-RAY DIFFRACTION18CHAIN F AND (RESID 55 THROUGH 125 )
19X-RAY DIFFRACTION19CHAIN F AND (RESID 126 THROUGH 250 )
20X-RAY DIFFRACTION20CHAIN G AND (RESID 4 THROUGH 36 )
21X-RAY DIFFRACTION21CHAIN G AND (RESID 37 THROUGH 163 )
22X-RAY DIFFRACTION22CHAIN G AND (RESID 164 THROUGH 251 )
23X-RAY DIFFRACTION23CHAIN H AND (RESID 1 THROUGH 36 )
24X-RAY DIFFRACTION24CHAIN H AND (RESID 37 THROUGH 147 )
25X-RAY DIFFRACTION25CHAIN H AND (RESID 148 THROUGH 251 )
26X-RAY DIFFRACTION26CHAIN I AND (RESID 4 THROUGH 36 )
27X-RAY DIFFRACTION27CHAIN I AND (RESID 37 THROUGH 250 )
28X-RAY DIFFRACTION28CHAIN J AND (RESID 4 THROUGH 54 )
29X-RAY DIFFRACTION29CHAIN J AND (RESID 55 THROUGH 147 )
30X-RAY DIFFRACTION30CHAIN J AND (RESID 148 THROUGH 251 )
31X-RAY DIFFRACTION31CHAIN K AND (RESID 4 THROUGH 36 )
32X-RAY DIFFRACTION32CHAIN K AND (RESID 37 THROUGH 125 )
33X-RAY DIFFRACTION33CHAIN K AND (RESID 126 THROUGH 204 )
34X-RAY DIFFRACTION34CHAIN K AND (RESID 205 THROUGH 252 )
35X-RAY DIFFRACTION35CHAIN L AND (RESID 4 THROUGH 36 )
36X-RAY DIFFRACTION36CHAIN L AND (RESID 37 THROUGH 125 )
37X-RAY DIFFRACTION37CHAIN L AND (RESID 126 THROUGH 250 )

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