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- PDB-4bgp: Crystal structure of La Crosse virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 4bgp
TitleCrystal structure of La Crosse virus nucleoprotein
ComponentsNUCLEOPROTEIN
KeywordsVIRAL PROTEIN / ORTHOBUNYAVIRUS / NUCLEOPROTEIN
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / symbiont-mediated suppression of host gene expression / 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 speciesLA CROSSE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsReguera, J. / Malet, H. / Weber, F. / Cusack, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural Basis for Encapsidation of Genomic RNA by La Crosse Orthobunyavirus Nucleoprotein
Authors: Reguera, J. / Malet, H. / Weber, F. / Cusack, S.
History
DepositionMar 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9814
Polymers26,6961
Non-polymers2843
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.590, 70.080, 70.730
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 NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / PROTEIN N / LA CROSSE VIRUS NUCLEOPROTEIN


Mass: 26696.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EXTRA G AT N-TERMINUS AFTER HIS-TAG CLEAVAGE / Source: (gene. exp.) LA CROSSE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04873
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsEXTRA G AT N-TERMINUS AFTER HIS-TAG CLEAVAGE

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.2 M LISO4, 0.1 M TRIS-HCL PH 8.5, 15% W/V PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29488 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.97
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.72 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
SHELXSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→46.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.171 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20409 1500 5.1 %RANDOM
Rwork0.18066 ---
obs0.18185 27988 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.342 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--0.97 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 16 230 2084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191932
X-RAY DIFFRACTIONr_bond_other_d0.0010.021814
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9562610
X-RAY DIFFRACTIONr_angle_other_deg0.78134175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.965234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41224.47996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66315331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6941511
X-RAY DIFFRACTIONr_chiral_restr0.0740.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212203
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 121 -
Rwork0.248 2036 -
obs--99.95 %

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