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- PDB-4idu: crystal structure of Schmallenberg virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 4idu
Titlecrystal structure of Schmallenberg virus nucleoprotein
Components(SBV nucleoprotein) x 2
KeywordsDNA BINDING PROTEIN / Schmallenberg virus / nucleoprotein / Protect genome RNA / replication and transcription
Function / homology
Function and homology information


viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
Bunyavirus nucleocapsid (N) protein, C-terminal domain / Poly(ADP-ribose) Polymerase; domain 1 - #20 / Bunyavirus nucleocapsid (N) protein / Bunyavirus nucleocapsid (N) , C-terminal domain / Bunyavirus nucleocapsid (N) , N-terminal domain / Bunyavirus nucleocapsid (N) protein / Poly(ADP-ribose) Polymerase; domain 1 / Cyclin A; domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSchmallenberg virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.08 Å
AuthorsDong, H. / Li, P. / Elliott, R.M. / Dong, C.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of Schmallenberg orthobunyavirus nucleoprotein suggests a novel mechanism of genome encapsidation
Authors: Dong, H. / Li, P. / Elliott, R.M. / Dong, C.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SBV nucleoprotein
B: SBV nucleoprotein
C: SBV nucleoprotein
D: SBV nucleoprotein


Theoretical massNumber of molelcules
Total (without water)104,9274
Polymers104,9274
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SBV nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,2081
Polymers26,2081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: SBV nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,3021
Polymers26,3021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: SBV nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,2081
Polymers26,2081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: SBV nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,2081
Polymers26,2081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.320, 86.440, 77.400
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SBV nucleoprotein


Mass: 26208.291 Da / Num. of mol.: 3 / Fragment: UNP residues 2-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schmallenberg virus / Gene: N / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: H2AM13
#2: Protein SBV nucleoprotein


Mass: 26302.082 Da / Num. of mol.: 1 / Fragment: UNP residues 2-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schmallenberg virus / Gene: N / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: H2AM13
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M sodium formate, 20% PEG3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9218 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 13, 2012
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9218 Å / Relative weight: 1
ReflectionResolution: 3.06→33.92 Å / Num. all: 18405 / Num. obs: 18304 / % possible obs: 99.4 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.09 / Net I/σ(I): 2
Reflection shellResolution: 3.06→3.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1260 / Rsym value: 0.76 / % possible all: 93.8

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Processing

Software
NameVersionClassification
EDNAdata collection
SHELXSphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.08→29.71 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.811 / SU B: 97.612 / SU ML: 0.799 / Cross valid method: THROUGHOUT / ESU R Free: 0.704 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.36425 960 5.1 %RANDOM
Rwork0.32051 ---
obs0.32283 17787 99.85 %-
all-18405 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.413 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.03 Å2
2---0.39 Å2-0 Å2
3---0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.025 Å
Luzzati d res low-4 Å
Luzzati sigma a0.36 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 3.08→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6838 0 0 0 6838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027012
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9349485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8565852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49424.037322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.188151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6231530
X-RAY DIFFRACTIONr_chiral_restr0.110.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215327
LS refinement shellResolution: 3.08→3.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 69 -
Rwork0.323 1234 -
obs--99.69 %
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)
12.1826-0.9925-0.28552.5905-0.60520.4043-0.04560.52410.1259-0.0203-0.09550.02870.1204-0.09250.14110.4443-0.04440.06490.54710.02810.221627.249516.33181.7095
21.23680.17230.25060.5628-0.07510.0767-0.02850.0072-0.0364-0.43480.08460.01530.0663-0.0038-0.05610.5685-0.04050.09630.4457-0.05880.453321.777637.625734.6023
32.82790.5419-0.37743.00420.00141.80130.0101-0.0357-0.2754-0.0226-0.0151-0.5355-0.1242-0.10180.00510.2823-0.02510.00820.2780.02570.48391.509-5.639633.4461
42.8110.4970.00971.5284-1.01812.44630.0641-0.01520.11730.02070.03910.2648-0.26760.3628-0.10330.37910.0244-0.030.39740.09220.2544-11.92621.02025.3579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 228
2X-RAY DIFFRACTION2B4 - 228
3X-RAY DIFFRACTION3C6 - 214
4X-RAY DIFFRACTION4D2 - 229

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