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- PDB-4h5o: Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein... -

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Basic information

Entry
Database: PDB / ID: 4h5o
TitleCrystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Pentamer Bound to Single-stranded RNA
Components
  • 35-mer poly(U) RNA
  • Nucleocapsid protein
KeywordsVIRAL PROTEIN/RNA / nucleocapsid protein / N protein / ribonucleoprotein / viral nucleoprotein / RNA binding / virus / RNP / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / host cell nucleus / RNA binding / identical protein binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesRift Valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsRaymond, D.D. / Smith, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Phleboviruses encapsidate their genomes by sequestering RNA bases.
Authors: Raymond, D.D. / Piper, M.E. / Gerrard, S.R. / Skiniotis, G. / Smith, J.L.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
F: Nucleocapsid protein
G: Nucleocapsid protein
H: Nucleocapsid protein
I: Nucleocapsid protein
J: Nucleocapsid protein
K: 35-mer poly(U) RNA
L: 35-mer poly(U) RNA


Theoretical massNumber of molelcules
Total (without water)295,00712
Polymers295,00712
Non-polymers00
Water00
1
A: Nucleocapsid protein
B: Nucleocapsid protein
D: Nucleocapsid protein
F: Nucleocapsid protein
G: Nucleocapsid protein
K: 35-mer poly(U) RNA


Theoretical massNumber of molelcules
Total (without water)147,5046
Polymers147,5046
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27240 Å2
ΔGint-253 kcal/mol
Surface area51830 Å2
MethodPISA
2
C: Nucleocapsid protein
E: Nucleocapsid protein
H: Nucleocapsid protein
I: Nucleocapsid protein
J: Nucleocapsid protein
L: 35-mer poly(U) RNA


Theoretical massNumber of molelcules
Total (without water)147,5046
Polymers147,5046
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27260 Å2
ΔGint-258 kcal/mol
Surface area52360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.810, 93.590, 124.780
Angle α, β, γ (deg.)101.700, 90.270, 114.180
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleocapsid protein


Mass: 27366.547 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift Valley fever virus / Strain: ZH-501 / Gene: N / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Ai/prare2 / References: UniProt: D3K5I7
#2: RNA chain 35-mer poly(U) RNA


Mass: 10670.844 Da / Num. of mol.: 2 / Source method: obtained synthetically

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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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% PEG3350, 280 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.9→121.596 Å / Num. all: 28961 / Num. obs: 28961 / % possible obs: 99.1 % / Redundancy: 2 % / Rsym value: 0.212 / Net I/σ(I): 2.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.9-4.1120.4631835641970.46399.1
4.11-4.3620.3491.8801440220.34999.2
4.36-4.6620.2942750337640.29499.2
4.66-5.0320.2542.3704635300.25499.4
5.03-5.5220.2482.3640632240.24899.3
5.52-6.1720.1942.6581229290.19499.5
6.17-7.1220.1713513225780.17199.6
7.12-8.7220.162.6433621830.1699.6
8.72-12.3320.1692.5327616680.16998.6
12.33-41.6011.90.211.916408660.2193.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
Blu-IceEpicsdata collection
MOSFLMdata reduction
PHASERphasing
BUSTER2.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LYF

3lyf


Resolution: 3.9→41.6 Å / Cor.coef. Fo:Fc: 0.5636 / Cor.coef. Fo:Fc free: 0.5121 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.776
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1459 5.04 %SHELL
Rwork0.228 ---
obs0.229 28958 99.17 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 55.482 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-10.9485 Å27.4022 Å27.6542 Å2
2---19.1423 Å217.4195 Å2
3---8.1938 Å2
Refine analyzeLuzzati coordinate error obs: 0.881 Å
Refinement stepCycle: LAST / Resolution: 3.9→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19084 1400 0 0 20484
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9583SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes478HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2908HARMONIC5
X-RAY DIFFRACTIONt_it21001HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2768SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24161SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d21001HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg28639HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion1.65
X-RAY DIFFRACTIONt_other_torsion3.19
LS refinement shellResolution: 3.9→4.04 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rwork0.2618 2804 -
all0.2618 --
obs--99.17 %
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)
1-0.78820.60751.63132.2652-1.40280.3834-0.0298-0.04760.1837-0.04-0.0209-0.0224-0.1576-0.23490.05070.0617-0.2864-0.1079-0.1757-0.0421-0.124731.355665.639810.9818
2-1.8363.1214-0.78381.70563.10591.49890.02930.262-0.1046-0.2312-0.04770.3720.05370.0570.0183-0.52240.00290.14690.4967-0.2025-0.27180.04756.077928.3966
34.4374-0.1916-0.7284-2.10253.36321.7423-0.0738-0.15320.08880.4141-0.1072-0.11120.08020.35680.18090.13920.0060.0098-0.0005-0.0654-0.472915.442661.258945.1026
4-0.3961-0.38023.09611.6861-1.144-0.54780.00250.17250.1346-0.12820.0008-0.1250.03820.1615-0.0033-0.1009-0.13610.0246-0.0161-0.2859-0.07418.0122-8.952816.0168
53.7227-1.911-2.64126.1362-0.06091.06220.0545-0.12-0.0318-0.0743-0.14520.25130.0226-0.42680.0907-0.2338-0.13580.08550.0362-0.1333-0.67631.268319.9372-2.8318
61.6273-0.85910.48150.8852-4.01133.2724-0.0296-0.2168-0.34470.52580.0388-0.48510.0194-0.009-0.0092-0.5012-0.08920.3008-0.01620.2464-0.507348.955211.53129.7662
71.2826-2.20192.3141-2.71517.2053.4896-0.0458-0.0071-0.44510.1789-0.0358-0.0359-0.04530.08160.0817-0.22990.10640.0202-0.02310.0217-0.20263.554844.16975.7364
810.4235-1.9566-0.1609-6.14745.87383.11040.0068-0.08320.02530.20230.00150.0273-0.2374-0.3146-0.0082-0.66990.1063-0.27410.077-0.1174-0.5498-13.246512.3193-6.6831
92.5775-0.19434.41046.1015-0.3777-0.45450.20720.31010.0144-0.3298-0.0232-0.223-0.3438-0.1631-0.184-0.3689-0.12530.0915-0.91840.13280.04885.823813.9442-20.2075
102.8937-2.93581.11044.49470.18594.72370.0163-0.11490.01370.00330.05260.02080.2666-0.1102-0.06880.02360.10710.09140.3191-0.05740.1893-4.86559.631939.608
111.47910.3221-0.1461.11270.53580.40120.02640.0120.0518-0.0394-0.08780.1334-0.1036-0.10490.0614-0.1315-0.04730.2807-0.154-0.0660.1042-12.404122.79434.7962
12-1.35881.8433-2.78630.26022.48251.09860.017-0.0657-0.04220.08110.02910.06290.0693-0.0195-0.04610.2602-0.1160.2721-0.1329-0.2194-0.3292-2.992725.257155.9047
130.9534-2.20141.98293.0881-0.40420.9602-0.07130.1493-0.13880.022-0.0446-0.1480.2114-0.21820.116-0.05730.1265-0.1591-0.09290.0969-0.0062-9.45061.6984-12.5501
142.2898-1.3177-1.3076-4.36374.46865.4167-0.0061-0.26710.10910.28050.06810.4869-0.0927-0.0315-0.062-0.4411-0.2158-0.27410.2646-0.399-0.421-40.564711.5487-29.5626
155.99910.173-0.0592-1.92082.4561.2319-0.03230.259-0.0526-0.3152-0.1537-0.25820.12740.21070.1860.0048-0.0576-0.09210.1838-0.1669-0.6862-25.40165.5209-46.2278
164.96290.7378-3.9811-1.3450.00424.47410.0308-0.17920.16610.1297-0.1060.2619-0.0589-0.13770.07520.25110.05750.02650.4896-0.02530.4349-14.44913.46543.3021
170.8221-0.96242.99720.0349-1.52074.0343-0.02670.14590.27-0.260.05080.3725-0.2081-0.1139-0.0241-0.5198-0.13910.01330.0458-0.0712-0.08339.02020.011216.4853
183.386-1.91810.8627-3.42893.27312.7374-0.0166-0.2956-0.21710.29090.13540.2764-0.1650.1773-0.1188-0.2217-0.0406-0.14570.0535-0.3114-0.342719.8257-4.30736.6047
192.11881.8615-0.78660.24112.32914.44690.0783-0.09020.1508-0.1051-0.010.08990.13270.0155-0.0683-0.22980.01690.17770.0748-0.1309-0.313942.911822.7276-7.0511
2010.33190.67150.8362-0.17911.16860.7865-0.0370.1562-0.0815-0.04520.0398-0.0861-0.0417-0.27-0.0029-0.82570.01510.5144-0.005-0.158-0.580927.369754.8025.3854
215.69240.08053.57975.63720.44822.33590.0456-0.4535-0.1620.1930.3071-0.11770.14530.1329-0.3527-0.5011-0.04420.1578-0.62390.0456-0.013746.448553.13218.8411
225.28332.7066-2.58473.7608-1.58714.0747-0.01770.09140.03350.00420.02490.0569-0.1396-0.126-0.00720.1399-0.1676-0.19890.246-0.1770.1704-45.48737.7639-40.6844
232.47510.06740.86431.1065-2.4628-0.5212-0.0099-0.0859-0.0530.0996-0.03470.17420.0821-0.09960.0446-0.0472-0.1162-0.4199-0.2526-0.13020.08-51.539244.8987-36.7838
24-1.72520.37364.77631.8997-0.2589-0.17460.01750.11310.1469-0.1089-0.0375-0.059-0.0989-0.02630.020.46850.0231-0.3117-0.1951-0.0432-0.3808-41.987441.7504-57.5228
25-0.34291.9162-3.85743.18510.48160.15250.0518-0.0838-0.01270.0668-0.02820.0468-0.0617-0.0087-0.0235-0.1561-0.0645-0.1462-0.2156-0.3257-0.1308-20.342676.1325-17.5689
264.09373.12663.47752.9797-0.5111.33940.06410.1321-0.14720.057-0.32620.47590.0707-0.55180.2621-0.0830.09270.1868-0.25840.0582-0.5275-8.049347.2251.5941
272.7724-2.6423.36020.2269-3.1576.82540.05840.28660.2346-0.4129-0.1257-0.3363-0.05460.01430.0673-0.4449-0.05990.0019-0.08120.4022-0.53369.771755.3065-11.0854
283.9080.37384.45591.1666-2.19645.63970.05090.1646-0.1598-0.2126-0.11310.28750.1359-0.21930.06220.46580.0019-0.10870.3668-0.03150.4549-53.16454.3561-45.0868
295.6747-0.3615-1.4881.2778-5.4465-1.6575-0.1798-0.0482-0.2320.33960.23550.52670.3837-0.1427-0.0557-0.63470.1192-0.01930.02050.0637-0.0562-29.450467.311-18.2041
301.99030.40640.9874-1.57173.5811.7414-0.03640.29220.2188-0.3870.02230.35480.2620.28660.0141-0.2573-0.06360.15570.1523-0.1926-0.2732-18.089271.373-38.1102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|5 - 34}A5 - 34
2X-RAY DIFFRACTION2{A|35 - 112}A35 - 112
3X-RAY DIFFRACTION3{A|113 - 245}A113 - 245
4X-RAY DIFFRACTION4{B|5 - 34}B5 - 34
5X-RAY DIFFRACTION5{B|35 - 112}B35 - 112
6X-RAY DIFFRACTION6{B|113 - 245}B113 - 245
7X-RAY DIFFRACTION7{C|5 - 34}C5 - 34
8X-RAY DIFFRACTION8{C|35 - 111}C35 - 111
9X-RAY DIFFRACTION9{C|112 - 245}C112 - 245
10X-RAY DIFFRACTION10{D|5 - 34}D5 - 34
11X-RAY DIFFRACTION11{D|35 - 111}D35 - 111
12X-RAY DIFFRACTION12{D|112 - 245}D112 - 245
13X-RAY DIFFRACTION13{E|5 - 34}E5 - 34
14X-RAY DIFFRACTION14{E|35 - 112}E35 - 112
15X-RAY DIFFRACTION15{E|113 - 245}E113 - 245
16X-RAY DIFFRACTION16{F|5 - 34}F5 - 34
17X-RAY DIFFRACTION17{F|35 - 112}F35 - 112
18X-RAY DIFFRACTION18{F|113 - 245}F113 - 245
19X-RAY DIFFRACTION19{G|5 - 34}G5 - 34
20X-RAY DIFFRACTION20{G|35 - 112}G35 - 112
21X-RAY DIFFRACTION21{G|113 - 245}G113 - 245
22X-RAY DIFFRACTION22{H|5 - 34}H5 - 34
23X-RAY DIFFRACTION23{H|35 - 112}H35 - 112
24X-RAY DIFFRACTION24{H|113 - 245}H113 - 245
25X-RAY DIFFRACTION25{I|5 - 34}I5 - 34
26X-RAY DIFFRACTION26{I|35 - 112}I35 - 112
27X-RAY DIFFRACTION27{I|113 - 245}I113 - 245
28X-RAY DIFFRACTION28{J|5 - 34}J5 - 34
29X-RAY DIFFRACTION29{J|35 - 112}J35 - 112
30X-RAY DIFFRACTION30{J|113 - 245}J113 - 245

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