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- PDB-2qvj: Crystal structure of a vesicular stomatitis virus nucleocapsid pr... -

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Basic information

Entry
Database: PDB / ID: 2qvj
TitleCrystal structure of a vesicular stomatitis virus nucleocapsid protein Ser290Trp mutant
ComponentsNucleocapsid protein
KeywordsRNA BINDING PROTEIN / nucleocapsid / Cytoplasm / Ribonucleoprotein / RNA-binding / Viral nucleoprotein / Virion
Function / homology
Function and homology information


RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLuo, M. / Green, T.J. / Zhang, X. / Tsao, J. / Qiu, S.
CitationJournal: J.Virol. / Year: 2008
Title: Role of intermolecular interactions of vesicular stomatitis virus nucleoprotein in RNA encapsidation.
Authors: Zhang, X. / Green, T.J. / Tsao, J. / Qiu, S. / Luo, M.
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)237,1595
Polymers237,1595
Non-polymers00
Water00
1
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein

A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)474,31910
Polymers474,31910
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area53660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.456, 236.652, 74.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a decamer consisting of the five copies of the N protein in the asymmetric unit plus an additional five copies created by rotation of the contents of the asymmetric unit by 180 degrees around the c-axis.

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Components

#1: Protein
Nucleocapsid protein / Protein N / Nucleoprotein / NP


Mass: 47431.883 Da / Num. of mol.: 5 / Mutation: S290W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Genus: Vesiculovirus / Strain: Indiana / Gene: N / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03521, UniProt: A6H4P1*PLUS

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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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5.5 % PEG 3350, 200 mM sodium chloride, 100mM sodium acetate, pH 4.5, vapor diffusion, hanging drop, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→41.62 Å / Num. obs: 54826 / % possible obs: 74.3 % / Redundancy: 4.62 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 19
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.172 / Num. unique all: 3262 / % possible all: 44.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.8→41.62 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.839 / SU B: 35.983 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2796 5.1 %RANDOM
Rwork0.243 ---
obs0.246 54826 74.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.198 Å2
Baniso -1Baniso -2Baniso -3
1-4.59 Å20 Å20 Å2
2---1.74 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16675 0 0 0 16675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02217065
X-RAY DIFFRACTIONr_angle_refined_deg0.9531.96323120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.47552100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7824.052765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.887152945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.55915100
X-RAY DIFFRACTIONr_chiral_restr0.0690.22510
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212945
X-RAY DIFFRACTIONr_nbd_refined0.1820.27536
X-RAY DIFFRACTIONr_nbtor_refined0.2970.211889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2363
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.2155
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.215
X-RAY DIFFRACTIONr_mcbond_it1.1261.510729
X-RAY DIFFRACTIONr_mcangle_it2.03216900
X-RAY DIFFRACTIONr_scbond_it0.87937294
X-RAY DIFFRACTIONr_scangle_it1.3794.56220
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 133 -
Rwork0.277 2172 -
all-2305 -
obs--42.79 %
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)
10.0012-0.0036-0.02180.09690.02350.43440.1411-0.015-0.051-0.0625-0.00520.0932-0.10830.0935-0.13590.109-0.07430.04230.0231-0.01890.003937.837146.541820.7444
211.3192-6.3224-1.85973.67381.68893.27320.37480.07920.16530.7477-0.19440.0949-0.01730.5199-0.18040.161-0.0416-0.0236-0.08480.0146-0.059952.10235.643838.3204
30.44620.0465-0.29230.01980.24875.3955-0.01180.10070.00010.10620.01310.06970.13760.2099-0.00140.2327-0.0046-0.0033-0.10570.00870.006157.67737.2232.1757
40.1458-0.7533-0.63363.89123.27282.7526-0.07180.12020.6465-0.1568-0.36210.11651.9191-0.57030.43390.3561-0.24740.07490.03950.02880.002843.173526.794931.9919
59.5532-0.57575.60065.03694.61418.1847-0.396-0.028-0.39350.55540.06990.95810.9762-0.76890.32610.1805-0.24090.19580.09280.04840.038439.743319.778735.013
60.1460.21630.21570.35110.2140.68360.0385-0.0007-0.09740.04230.02050.032-0.02960.0405-0.059-0.00670.0270.01460.0429-0.01730.000241.339231.58739.6092
72.4016-2.0856-0.75993.16972.25392.11070.0590.58190.0593-0.5989-0.29620.0114-0.1274-0.21220.23720.0297-0.1590.0260.10360.13270.025843.911113.9972-19.8498
81.02310.3886-1.73463.3875-1.64973.244-0.08110.1423-0.1285-0.04380.09210.20480.1595-0.181-0.011-0.1957-0.0355-0.06230.05610.00890.031924.803922.516-5.2468
91.0045-0.12351.19050.1331-0.41342.01560.0206-0.05410.0325-0.0277-0.06220.0213-0.01380.04380.04160.1070.10580.11130.0225-0.0659-0.06123.012359.632220.7106
104.01390.9263-1.52441.85540.63771.79790.1445-0.2007-0.19890.0597-0.0271-0.1723-0.07410.3647-0.1173-0.0818-0.02970.0049-0.0193-0.0244-0.044126.215564.216428.0352
110.2424-0.636-0.1562.11660.26684.8695-0.0061-0.0088-0.00650.1991-0.14050.05550.42970.03430.1466-0.1565-0.00030.1140.01640.02840.009418.855854.04837.67
120.6628-1.5554-0.278913.87792.75634.1456-0.1314-0.4497-0.77160.86990.09910.42981.8111-0.02140.03220.1678-0.03740.0940.01990.0168-0.075420.886338.777735.2509
130.35120.41170.98721.17021.43962.891-0.05450.0848-0.0540.1263-0.01760.05830.3639-0.05210.0721-0.07070.01270.0310.0648-0.00530.016820.06552.586923.0262
140.46160.45650.4251.3390.59490.81880.04210.0071-0.0528-0.0709-0.0835-0.0117-0.2956-0.16410.0414-0.07570.0517-0.03710.08650.0147-0.049112.24552.84385.2681
152.3322-0.897-0.85010.34810.2980.5747-0.0142-0.0442-0.0752-0.088-0.1141-0.0119-0.1338-0.05260.1283-0.0669-0.0085-0.04220.0694-0.0054-0.022916.682537.8763-4.2608
162.54150.70420.16672.2265-1.75521.60840.09270.3008-0.3677-0.5127-0.06420.12210.22270.1851-0.02850.03760.0195-0.03270.0059-0.04020.01379.748633.6843-9.4229
170.0777-0.1711-0.03370.4376-0.09690.4929-0.04980.00920.1085-0.0832-0.11610.0117-0.0275-0.00830.1659-0.01170.00170.02820.0340.0141-0.0213-32.589950.234720.9104
180.1417-0.3483-0.36460.85590.89590.93790.1361-0.1109-0.06120.08450.1848-0.0396-0.51480.0051-0.3209-0.0362-0.08170.01350.18810.0754-0.027-16.27568.013427.7399
190.6585-0.7903-0.98892.86831.51933.4066-0.11710.0384-0.3855-0.13440.07030.19890.06840.36980.0468-0.06630.0320.0092-0.01150.0381-0.0267-15.916654.982838.9164
204.34934.28633.572315.049110.515912.19630.2732-0.56-0.8396-0.3612-0.1285-0.39330.87240.1474-0.14470.07280.2701-0.00440.08480.1024-0.0636-6.596543.34334.6781
210.00830.07120.12150.60761.03731.7709-0.0127-0.0563-0.0872-0.20980.20060.02370.30460.3436-0.1878-0.00590.04740.02520.13110.0122-0.0472-14.158454.055121.8417
220.1243-0.5583-0.3252.50721.45960.84980.11270.00350.04390.0206-0.0452-0.02410.0637-0.0263-0.06740.0045-0.0016-0.01860.04340.0163-0.03-20.223845.51033.9526
238.31181.67680.4430.34390.0750.06060.15161.0950.105-0.0633-0.02940.10590.35570.1416-0.12220.1935-0.011-0.05580.2121-0.0372-0.0938-0.712245.0443-18.0416
241.3290.8826-0.28970.5864-0.22052.5317-0.09560.1334-0.1658-0.1268-0.0799-0.16680.4143-0.19610.1755-0.03620.0412-0.0152-0.0046-0.0350.0323-13.965629.5299-4.9121
250.74751.05740.49391.51640.67770.3479-0.0760.16790.2665-0.02720.15740.22040.25990.144-0.08140.04070.0133-0.03270.12870.0189-0.1528-61.006516.0819.5373
260.6848-0.36640.56280.2987-0.24332.55030.0495-0.20420.18540.1395-0.0201-0.0631-0.2364-0.294-0.0294-0.02270.0043-0.0362-0.0004-0.0264-0.0032-49.521141.169634.5801
270.8241-1.32380.79564.2777-0.12383.93220.1623-0.00390.02040.1866-0.07260.1777-0.01330.3273-0.0897-0.0898-0.0007-0.0314-0.0552-0.0485-0.0278-45.834535.558937.6063
288.91044.283-1.9563.5969-1.66297.86490.1593-0.4576-0.5488-0.0072-0.6647-0.03390.14622.17330.50540.03060.1197-0.15480.24570.0623-0.1291-30.54630.52234.8815
290.16190.21530.01520.72210.86631.64440.11090.04660.11120.06030.0526-0.02490.18710.0952-0.16350.02140.0325-0.03780.05790.0093-0.0182-45.149933.326114.1628
300.01640.07440.09560.33740.43360.5572-0.1859-0.02420.12910.05490.1033-0.01410.0929-0.05440.0825-0.01370.0161-0.00930.0760.0247-0.0302-38.412424.24373.2959
315.09649.8155-1.769918.9212-3.21662.8137-0.64790.26250.3057-0.93551.07990.26541.12850.3866-0.4320.09820.161-0.06860.0189-0.01350.0723-27.369334.7759-21.4127
322.3996-0.8072.20233.4452-1.50824.57520.1570.2784-0.2405-0.22180.0197-0.25580.26040.3907-0.1767-0.05960.02120.0242-0.0484-0.05660.0191-29.355316.0629-5.0016
330.4585-0.94960.90792.1774-1.97811.8431-0.14440.2457-0.00340.4887-0.1639-0.0127-0.44230.18160.3084-0.0039-0.0177-0.06760.0848-0.0333-0.017759.15322.424710.112
340.8128-0.8598-0.20511.12330.98142.78530.0539-0.13090.04020.1168-0.1849-0.09780.70430.05420.1310.2443-0.0434-0.02240.0237-0.0711-0.005461.0548-2.516741.8577
351.2469-0.2574-2.05971.4635-0.51814.0331-0.00110.26420.25390.4833-0.0622-0.23020.4160.09320.06330.0333-0.0181-0.05650.0169-0.0638-0.055864.8593-3.584432.8749
362.67633.7816-0.31495.3487-0.58063.43230.18230.16920.7870.6562-0.02250.46680.1512-0.8599-0.15990.063-0.10040.07770.2513-0.27360.042446.0879-3.430334.2135
370.5552-0.13471.21670.1953-0.30322.6666-0.0115-0.06120.1125-0.00470.0124-0.07870.249-0.1215-0.001-0.00330.0040.02530.049-0.0494-0.041557.8909-0.339512.4563
382.3391.69161.01495.7144-0.09970.59510.0841-0.2375-0.1494-0.0948-0.04090.1649-0.3679-0.0069-0.0431-0.1019-0.0170.01660.0075-0.0122-0.060942.29315.0291.8584
398.8572-12.2796-0.493418.0979-1.54034.63740.58870.57010.1309-1.4227-0.51830.08430.4661-0.9377-0.0704-0.0177-0.09220.00580.2150.0689-0.137243.8781-15.693-19.3799
401.00670.8949-0.12432.51270.67481.0735-0.03710.07170.2967-0.33810.0690.50440.23430.1358-0.0319-0.1150.0623-0.05210.02060.04140.004634.28933.6602-5.5323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 641 - 63
2X-RAY DIFFRACTION2AA65 - 8064 - 79
3X-RAY DIFFRACTION3AA81 - 13280 - 131
4X-RAY DIFFRACTION4AA133 - 148132 - 147
5X-RAY DIFFRACTION5AA149 - 180148 - 179
6X-RAY DIFFRACTION6AA181 - 346180 - 345
7X-RAY DIFFRACTION7AA347 - 374346 - 373
8X-RAY DIFFRACTION8AA375 - 422374 - 421
9X-RAY DIFFRACTION9BB2 - 641 - 63
10X-RAY DIFFRACTION10BB65 - 10364 - 102
11X-RAY DIFFRACTION11BB104 - 149103 - 148
12X-RAY DIFFRACTION12BB150 - 179149 - 178
13X-RAY DIFFRACTION13BB180 - 235179 - 234
14X-RAY DIFFRACTION14BB236 - 306235 - 305
15X-RAY DIFFRACTION15BB307 - 355306 - 354
16X-RAY DIFFRACTION16BB356 - 422355 - 421
17X-RAY DIFFRACTION17CC2 - 651 - 64
18X-RAY DIFFRACTION18CC66 - 10665 - 105
19X-RAY DIFFRACTION19CC107 - 147106 - 146
20X-RAY DIFFRACTION20CC148 - 179147 - 178
21X-RAY DIFFRACTION21CC180 - 238179 - 237
22X-RAY DIFFRACTION22CC239 - 338238 - 337
23X-RAY DIFFRACTION23CC339 - 376338 - 375
24X-RAY DIFFRACTION24CC377 - 422376 - 421
25X-RAY DIFFRACTION25DD2 - 441 - 43
26X-RAY DIFFRACTION26DD45 - 10144 - 100
27X-RAY DIFFRACTION27DD102 - 148101 - 147
28X-RAY DIFFRACTION28DD149 - 179148 - 178
29X-RAY DIFFRACTION29DD180 - 276179 - 275
30X-RAY DIFFRACTION30DD277 - 349276 - 348
31X-RAY DIFFRACTION31DD350 - 374349 - 373
32X-RAY DIFFRACTION32DD375 - 422374 - 421
33X-RAY DIFFRACTION33EE2 - 451 - 44
34X-RAY DIFFRACTION34EE46 - 8345 - 82
35X-RAY DIFFRACTION35EE84 - 14583 - 144
36X-RAY DIFFRACTION36EE146 - 190145 - 189
37X-RAY DIFFRACTION37EE191 - 288190 - 287
38X-RAY DIFFRACTION38EE289 - 342288 - 341
39X-RAY DIFFRACTION39EE343 - 372342 - 371
40X-RAY DIFFRACTION40EE373 - 422372 - 421

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