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- PDB-4h5q: Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein... -

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Basic information

Entry
Database: PDB / ID: 4h5q
TitleCrystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Hexamer Bound to Single-stranded DNA
Components
  • 30-mer poly(T) DNA
  • Nucleocapsid proteinVirus
KeywordsVIRAL PROTEIN/DNA / nucleocapsid protein / N protein / ribonucleoprotein / viral nucleoprotein / RNA binding / virus / RNP / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / 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
DNA / DNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesRift valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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: 30-mer poly(T) DNA


Theoretical massNumber of molelcules
Total (without water)86,3134
Polymers86,3134
Non-polymers00
Water1,00956
1
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: 30-mer poly(T) DNA

A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: 30-mer poly(T) DNA


Theoretical massNumber of molelcules
Total (without water)172,6278
Polymers172,6278
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area31250 Å2
ΔGint-202 kcal/mol
Surface area60230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.640, 108.640, 261.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-302-

HOH

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Components

#1: Protein Nucleocapsid protein / Virus


Mass: 27366.547 Da / Num. of mol.: 3
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: DNA chain 30-mer poly(T) DNA


Mass: 4213.742 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEACH DNA CHAIN IS MODELED WITH ONLY 14 BASES. ADDITIONAL BASES IN THE DNA STRAND ARE SUPPLIED BY SYMMETRY.

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG3350, 350 mM sodium chloride, 100 mM Bis-Tris, pH 5.5, 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: 2.7→94.085 Å / Num. all: 25771 / Num. obs: 25771 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rsym value: 0.114 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.854.30.77911549036150.77998.5
2.85-3.024.50.5611.31570435050.56199.8
3.02-3.234.50.3462.21468332710.34699.8
3.23-3.494.50.1953.91377230860.19599.9
3.49-3.824.50.1196.21271128500.119100
3.82-4.274.40.0739.81151226070.073100
4.27-4.934.40.05911.21018023320.059100
4.93-6.044.30.097.3862620100.09100
6.04-8.544.20.04114.6667815930.04199.9
8.54-53.65840.03116.835879020.03195.5

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3lyf


Resolution: 2.7→53.66 Å / Cor.coef. Fo:Fc: 0.9422 / Cor.coef. Fo:Fc free: 0.9175 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.982 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.517 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.3
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1313 5.1 %RANDOM
Rwork0.1891 ---
obs0.1911 25749 99.29 %-
Displacement parametersBiso max: 151.99 Å2 / Biso mean: 61.0411 Å2 / Biso min: 16.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.9209 Å20 Å20 Å2
2---0.9209 Å20 Å2
3---1.8418 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.7→53.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5698 277 0 56 6031
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2920SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes862HARMONIC5
X-RAY DIFFRACTIONt_it6113HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion785SEMIHARMONIC5
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_contact7043SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6113HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8308HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion3.24
LS refinement shellResolution: 2.7→2.81 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2658 155 5.58 %
Rwork0.2294 2623 -
all0.2315 2778 -
obs--99.29 %
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)
12.7221-0.47211.19120.4704-0.38322.82610.07810.03350.0183-0.0926-0.023-0.37080.33540.4288-0.0551-0.02180.19340.0228-0.0978-0.09460.157916.219540.6898-15.4384
24.6162-2.51671.28484.25340.26012.2648-0.1975-0.5263-0.0720.25080.2528-0.2304-0.174-0.1003-0.0553-0.03810.1027-0.0144-0.10630.006-0.0874-10.442411.6158-9.6972
32.94610.6181-0.89991.7729-0.1512.21130.01790.14160.0443-0.16160.0529-0.1609-0.2380.1278-0.07080.010.02090.0512-0.1301-0.0225-0.1156-8.32323.974-29.1767
4-0.1996-0.03920.84441.7081-0.46150-0.0184-0.0117-0.01310.03030.0289-0.0451-0.02060.0137-0.01040.258-0.06270.061-0.13620.0729-0.06873.16585.2258-29.5774
50.09580.93770.2784.0010.4750.21580.0223-0.0769-0.215-0.00660.05820.0990.0176-0.2448-0.0805-0.06880.13710.0051-0.03570.01270.0023-22.13915.104-18.4349
61.7021-0.426-0.5723.234-0.1843.21340.0759-0.09040.07890.1983-0.1129-0.102-0.03850.05780.037-0.07390.05450.0291-0.0970.0252-0.0359-48.186214.9733-12.4162
73.5558-0.32410.17252.2521-0.3981.57240.03860.11970.0446-0.0425-0.0674-0.17610.05070.0490.02880.02430.07170.045-0.08880.0387-0.1514-35.721216.1514-31.181
82.7102-1.63662.47221.3309-0.27510.3396-0.07590.27810.1922-0.05490.0024-0.0611-0.12330.17670.07340.05650.0236-0.0023-0.051-0.0247-0.04360.102980.9106-20.0335
94.15571.3978-0.23534.65560.85193.2846-0.149-0.50460.16110.46010.0529-0.6060.32610.22970.09610.03980.1328-0.0825-0.122-0.0442-0.080210.435746.2816-6.3399
103.3680.7044-0.71094.46280.81224.1617-0.0855-0.01130.1376-0.20930.0682-0.1042-0.2862-0.00750.01730.04530.06250.042-0.2258-0.0108-0.19584.112650.5427-28.2454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|4 - 33}A4 - 33
2X-RAY DIFFRACTION2{A|34 - 117}A34 - 117
3X-RAY DIFFRACTION3{A|118 - 245}A118 - 245
4X-RAY DIFFRACTION4{B|5 - 12}B5 - 12
5X-RAY DIFFRACTION5{B|17 - 34}B17 - 34
6X-RAY DIFFRACTION6{B|35 - 127}B35 - 127
7X-RAY DIFFRACTION7{B|128 - 245}B128 - 245
8X-RAY DIFFRACTION8{C|4 - 33}C4 - 33
9X-RAY DIFFRACTION9{C|34 - 112}C34 - 112
10X-RAY DIFFRACTION10{C|113 - 245}C113 - 245

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