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- PDB-3u3i: A RNA binding protein from Crimean-Congo hemorrhagic fever virus -

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Basic information

Entry
Database: PDB / ID: 3u3i
TitleA RNA binding protein from Crimean-Congo hemorrhagic fever virus
ComponentsNucleocapsid protein
KeywordsRNA BINDING PROTEIN / nucleocapsid protein / endonuclease / RNA binding / CCHFV
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1110 / Nucleocapsid N protein / Nucleocapsid N protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCrimean-Congo hemorrhagic fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.304 Å
AuthorsGuo, Y. / Wang, W.M. / Ji, W. / Deng, M. / Sun, Y.N. / Lou, Z.Y. / Rao, Z.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crimean-Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses
Authors: Guo, Y. / Wang, W.M. / Ji, W. / Deng, M. / Sun, Y.N. / Zhou, H. / Yang, C. / Deng, F. / Wang, H. / Hu, Z. / Lou, Z.Y. / Rao, Z.H.
History
DepositionOct 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)53,9841
Polymers53,9841
Non-polymers00
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.339, 67.898, 131.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleocapsid protein


Mass: 53984.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HLI8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: KCl, 20%(w/v) PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22556 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.46 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX1.6.1_357refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.304→43.639 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7912 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 1067 5.03 %RANDOM
Rwork0.2239 20145 --
obs0.2256 21212 89.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.356 Å2 / ksol: 0.275 e/Å3
Displacement parametersBiso max: 209.3 Å2 / Biso mean: 49.847 Å2 / Biso min: 11.6 Å2
Baniso -1Baniso -2Baniso -3
1-16.3307 Å2-0 Å2-0 Å2
2---5.8622 Å20 Å2
3----10.4684 Å2
Refinement stepCycle: LAST / Resolution: 2.304→43.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 0 369 3995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0253717
X-RAY DIFFRACTIONf_angle_d2.4615016
X-RAY DIFFRACTIONf_chiral_restr0.169551
X-RAY DIFFRACTIONf_plane_restr0.012641
X-RAY DIFFRACTIONf_dihedral_angle_d21.291371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3037-2.40850.27791130.23562461257488
2.4085-2.53550.23311490.22152556270593
2.5355-2.69430.27471250.2242525265090
2.6943-2.90230.29461340.24032645277995
2.9023-3.19430.26551340.24122768290298
3.1943-3.65630.28091180.22212242236091
3.6563-4.60570.22451280.19072006213481
4.6057-43.64650.2381660.20872942310899
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)
10.1737-0.00910.28250.02530.3160.8086-0.0087-0.06090.0223-0.03330.0036-0.01990.1154-0.08970.0070.1733-0.0421-0.0020.12380.00410.152214.7225-11.0635-31.0937
20.4440.17470.00280.13620.03040.08410.0072-0.0368-0.0364-0.04150.0203-0.0136-0.0291-0.0118-0.02040.1169-0.0314-0.01180.16240.03410.141716.4533-11.3822-30.5784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:479)A1 - 479
2X-RAY DIFFRACTION2(chain A and resid 483:870)A483 - 870

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