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- PDB-4h5l: Crystal Structure of Toscana Virus Nucleocapsid Protein Hexamer -

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Basic information

Entry
Database: PDB / ID: 4h5l
TitleCrystal Structure of Toscana Virus Nucleocapsid Protein Hexamer
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / nucleocapsid protein / N protein / ribonucleoprotein / viral nucleoprotein / RNA binding / virus / RNP
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 / molecular replacement / Resolution: 2.75 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: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)166,4416
Polymers166,4416
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19320 Å2
ΔGint-140 kcal/mol
Surface area64880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.350, 93.750, 95.520
Angle α, β, γ (deg.)67.920, 85.940, 87.950
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 27740.109 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toscana virus / Strain: ISS Ph1.3 / Gene: N / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Ai/prare2 / References: UniProt: P21701
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23% isopropanol, 280 mM magnesium chloride, 100 mM HEPES, pH 7.5, 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: 2.75→88.345 Å / Num. all: 39945 / Num. obs: 39945 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Redundancy: 1.9 % / Rsym value: 0.086 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.75-2.90.4741.41078757460.47494.2
2.9-3.070.3721.81043654990.37294.6
3.07-3.290.2492.7988751900.24995
3.29-3.550.1733.4924748260.17395.2
3.55-3.890.1026.3862444950.10295.4
3.89-4.350.0626.3772640010.06295.6
4.35-5.020.05112.9694935870.05195.8
5.02-6.150.05113.6579929880.05195.8
6.15-8.70.03715.6453923460.03796.3
8.7-50.2210.02622.6245312670.02695.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.11data extraction
Blu-IceEpicsdata collection
MOSFLMdata reduction
BUSTER2.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LYF

3lyf


Resolution: 2.75→50.22 Å / Cor.coef. Fo:Fc: 0.9071 / Cor.coef. Fo:Fc free: 0.9005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 2022 5.06 %RANDOM
Rwork0.2189 ---
obs0.2199 39944 95.2 %-
all-39945 --
Displacement parametersBiso max: 287.88 Å2 / Biso mean: 82.9153 Å2 / Biso min: 9.59 Å2
Baniso -1Baniso -2Baniso -3
1--11.0955 Å2-3.833 Å20.0928 Å2
2--5.5626 Å2-4.9667 Å2
3---5.533 Å2
Refine analyzeLuzzati coordinate error obs: 0.531 Å
Refinement stepCycle: LAST / Resolution: 2.75→50.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11221 0 0 17 11238
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5411SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes257HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1659HARMONIC5
X-RAY DIFFRACTIONt_it11412HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1542SEMIHARMONIC5
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_contact13527SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11412HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg15415HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion3.07
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2534 160 5.47 %
Rwork0.2475 2763 -
all0.2478 2923 -
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)
11.4633-0.2915-1.18122.43691.77711.3151-0.0612-0.079-0.1876-0.30950.04070.0664-0.3070.16810.02050.2360.21450.0706-0.02830.0768-0.082517.546-25.1037-68.4973
20.6684-0.2761-0.37522.4734-0.07070.96370.1168-0.1482-0.14910.14830.0578-0.2932-0.30850.0026-0.17460.18960.17970.0111-0.1183-0.0121-0.149110.45527.7528-73.3617
3-0.0106-0.0057-0.07860.19760.17-0.14120.01330.1140.046-0.0364-0.1061-0.06990.11870.05780.09270.42470.2360.141-0.25480.0057-0.4316-6.930420.3499-74.5339
41.31550.4167-0.26960.959-0.19941.8546-0.21990.00290.00810.33980.2433-0.14050.39080.285-0.02340.2880.3097-0.0101-0.2379-0.0225-0.2958-6.699135.4165-52.5345
50.4054-1.00830.43851.00530.26994.7832-0.1042-0.0772-0.19080.11360.21840.1437-0.1504-0.021-0.11420.34150.22770.0958-0.13380.1089-0.2161-19.965839.0549-51.0646
61.1998-0.46311.0061.8839-1.30340.6132-0.16770.27510.3470.0209-0.1644-0.46430.0074-0.12820.33210.20340.318-0.0099-0.13260.1358-0.0763-17.033227.6546-19.295
70.0425-0.60490.6910.8737-1.18951.08990.08860.0421-0.0880.09690.03490.0493-0.1913-0.3885-0.12340.18140.29990.0346-0.12680.0702-0.1505-23.752311.6407-6.2073
81.54660.30230.24931.2074-0.41041.66320.03210.07980.325-0.4223-0.18350.12320.20850.35740.15140.18190.1748-0.02930.01490.0229-0.1042-2.5744-1.3676-1.113
92.747-1.7879-0.88470.9315-0.10180.98320.0322-0.3086-0.2961-0.1957-0.0923-0.12890.39040.09220.06020.29630.16520.0652-0.03980.0319-0.2045-6.4561-13.84383.4821
100.97780.00050.44331.60110.11150.4439-0.25290.1479-0.06310.46240.18-0.2282-0.4771-0.09260.0730.27550.1697-0.1711-0.1642-0.0134-0.262913.7415-29.6782-21.1867
110.00791.7762-0.9374-3.1956-3.22675.5111-0.2089-0.025-0.03050.7840.3797-0.0296-0.01560.138-0.17070.32030.27680.0649-0.24820.0913-0.216110.6634-39.1492-40.0573
122.2830.8298-0.32831.26340.19150.6735-0.0937-0.6489-0.11420.27890.0201-0.2488-0.09360.07950.07360.12010.115-0.09970.13970.046-0.087921.1973-22.3915-55.4053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|5 - 36}A5 - 36
2X-RAY DIFFRACTION2{A|37 - 248}A37 - 248
3X-RAY DIFFRACTION3{B|6 - 54}B6 - 54
4X-RAY DIFFRACTION4{B|55 - 249}B55 - 249
5X-RAY DIFFRACTION5{C|5 - 36}C5 - 36
6X-RAY DIFFRACTION6{C|37 - 248}C37 - 248
7X-RAY DIFFRACTION7{D|5 - 54}D5 - 54
8X-RAY DIFFRACTION8{D|55 - 248}D55 - 248
9X-RAY DIFFRACTION9{E|5 - 36}E5 - 36
10X-RAY DIFFRACTION10{E|37 - 248}E37 - 248
11X-RAY DIFFRACTION11{F|5 - 54}F5 - 54
12X-RAY DIFFRACTION12{F|55 - 248}F55 - 248

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