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- PDB-4h5p: Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein... -

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Basic information

Entry
Database: PDB / ID: 4h5p
TitleCrystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Tetramer Bound to Single-stranded RNA
Components
  • 28-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


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
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesRift Valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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: 28-mer poly(U) RNA
F: 28-mer poly(U) RNA


Theoretical massNumber of molelcules
Total (without water)117,9496
Polymers117,9496
Non-polymers00
Water9,818545
1
A: Nucleocapsid protein
B: Nucleocapsid protein
E: 28-mer poly(U) RNA

A: Nucleocapsid protein
B: Nucleocapsid protein
E: 28-mer poly(U) RNA


Theoretical massNumber of molelcules
Total (without water)117,9496
Polymers117,9496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area22160 Å2
ΔGint-208 kcal/mol
Surface area41340 Å2
MethodPISA
2
C: Nucleocapsid protein
D: Nucleocapsid protein
F: 28-mer poly(U) RNA

C: Nucleocapsid protein
D: Nucleocapsid protein
F: 28-mer poly(U) RNA


Theoretical massNumber of molelcules
Total (without water)117,9496
Polymers117,9496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area22380 Å2
ΔGint-211 kcal/mol
Surface area41170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.640, 193.180, 77.420
Angle α, β, γ (deg.)90.000, 108.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nucleocapsid protein


Mass: 27366.547 Da / Num. of mol.: 4
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 28-mer poly(U) RNA


Mass: 4241.363 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEACH RNA CHAIN IS MODELED WITH ONLY 14 BASES. ADDITIONAL BASES IN THE RNA 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% 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: 2.15→96.59 Å / Num. all: 55733 / Num. obs: 55733 / % possible obs: 95.5 % / Redundancy: 3.7 % / Rsym value: 0.111 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.273.30.5841.32189666380.58477.9
2.27-2.43.60.4521.62830878640.45297.8
2.4-2.573.70.3372.22714374020.33798
2.57-2.783.70.2333.12560669240.23398.3
2.78-3.043.80.1574.62401063810.15798.7
3.04-3.43.90.1017.12237957980.10198.7
3.4-3.933.90.06510.21993251500.06599.2
3.93-4.813.80.05311.51669043410.05399.3
4.81-6.83.90.05311.91305933660.05399.3
6.8-48.4233.80.0456.6709218690.04599.1

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Processing

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

3lyf


Resolution: 2.15→31.48 Å / Cor.coef. Fo:Fc: 0.9411 / Cor.coef. Fo:Fc free: 0.9232 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.258 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2827 5.07 %RANDOM
Rwork0.1803 ---
obs0.1822 55716 95.46 %-
Displacement parametersBiso max: 135.96 Å2 / Biso mean: 39.1499 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.1021 Å20 Å2-2.7084 Å2
2--3.0081 Å20 Å2
3----4.1102 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.15→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7640 559 0 545 8744
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3826SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes190HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1164HARMONIC5
X-RAY DIFFRACTIONt_it8397HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1108SEMIHARMONIC5
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_contact10327SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8397HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg11448HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion2.92
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2592 148 4.95 %
Rwork0.2175 2843 -
all0.2196 2991 -
obs--95.46 %
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)
12.03780.8368-1.35920.9359-0.61321.92940.01420.5998-0.3675-0.08290.20750.12920.279-0.0936-0.2217-0.1586-0.023-0.01940.1263-0.07050.057515.471923.6725-24.044
23.68560.31510.18011.39060.3371.8674-0.0489-0.21610.3265-0.0155-0.0743-0.08880.15460.07090.1232-0.1580.01150.0384-0.1194-0.0142-0.056219.173319.263813.9164
35.07320.67061.31472.98530.08353.0583-0.3645-0.20791.5145-0.0466-0.01660.6398-0.44550.01890.3812-0.26560.0063-0.0849-0.3544-0.08840.565712.519441.50713.2756
45.35861.20342.9551.32670.19092.0479-0.0745-0.57070.19120.2429-0.28220.33620.0787-0.33170.3567-0.1882-0.03190.09280.0421-0.16230.060114.603523.91623.1986
54.52230.1091-1.56161.5256-0.08112.9536-0.1284-0.0859-0.8327-0.0763-0.0342-0.03830.2891-0.01890.1625-0.15810.0011-0.0086-0.0907-0.02140.09952.884419.233219.6577
64.7267-0.6552-1.05972.7420.25431.92230.2025-0.41740.6036-0.01610.0799-0.1339-0.26410.0573-0.2824-0.1605-0.01720.0034-0.0708-0.0784-0.008952.470941.356526.8005
77.0137-0.7714-1.44761.33421.18161.1159-0.077-0.46750.1950.24550.1719-0.0172-0.15790.5008-0.0949-0.0466-0.0495-0.01720.18430.0146-0.256227.6794-7.3789-6.8374
81.78080.1765-0.51580.7740.23732.4029-0.00780.16310.1731-0.0514-0.0099-0.10510.0530.01870.0177-0.02740.00330.043-0.04580.0044-0.101-7.101-2.4494-22.5453
92.5743-0.4127-0.12413.0129-0.18871.0745-0.08970.0342-0.46050.30560.0660.1420.2227-0.02820.02380.1111-0.0120.1134-0.1371-0.0165-0.0587-8.4224-24.936-16.4262
100.29030.37690.551.5407-1.11934.8480.08030.02270.0998-0.1-0.1739-0.2150.05770.60530.0936-0.05860.06310.09280.06490.0417-0.122242.4646-7.3232-52.0566
116.0946-0.3851-2.04071.3149-0.36013.45090.1419-0.0980.41530.0337-0.00160.0492-0.41830.0085-0.14030.0055-0.00390.0423-0.0903-0.0135-0.146526.6245-2.4056-16.9125
125.25890.5314-0.90963.39580.3492.5341-0.2582-0.4657-1.48790.27880.0109-0.06720.43180.29210.2473-0.0990.03260.0588-0.19490.13240.082433.7388-24.5723-15.7033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 34}A2 - 34
2X-RAY DIFFRACTION2{A|35 - 112}A35 - 112
3X-RAY DIFFRACTION3{A|113 - 245}A113 - 245
4X-RAY DIFFRACTION4{B|2 - 34}B2 - 34
5X-RAY DIFFRACTION5{B|35 - 112}B35 - 112
6X-RAY DIFFRACTION6{B|113 - 245}B113 - 245
7X-RAY DIFFRACTION7{C|2 - 34}C2 - 34
8X-RAY DIFFRACTION8{C|35 - 111}C35 - 111
9X-RAY DIFFRACTION9{C|112 - 245}C112 - 245
10X-RAY DIFFRACTION10{D|2 - 34}D2 - 34
11X-RAY DIFFRACTION11{D|35 - 111}D35 - 111
12X-RAY DIFFRACTION12{D|112 - 245}D112 - 245

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