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- PDB-4bhh: Crystal structure of tetramer of La Crosse virus nucleoprotein in... -

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Basic information

Entry
Database: PDB / ID: 4bhh
TitleCrystal structure of tetramer of La Crosse virus nucleoprotein in complex with ssRNA
Components
  • NUCLEOPROTEIN
  • POLY-URIDINE 45-MER
KeywordsVIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA COMPLEX / RNA-BINDING / GENOME PACKAGING
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / symbiont-mediated suppression of host gene expression / 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
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesLA CROSSE VIRUS
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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
DepositionApr 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: NUCLEOPROTEIN
D: NUCLEOPROTEIN
F: NUCLEOPROTEIN
R: POLY-URIDINE 45-MER
Z: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)120,2145
Polymers120,2145
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-175.7 kcal/mol
Surface area46220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.950, 86.460, 90.190
Angle α, β, γ (deg.)90.00, 106.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21F
12D
22Z
13B
23F
14D
24Z

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUBA19 - 21220 - 213
21PROPROLEULEUFC19 - 21220 - 213
12PROPROLEULEUDB19 - 21220 - 213
22PROPROLEULEUZE19 - 21220 - 213
13ASPASPGLYGLYBA221 - 231222 - 232
23ASPASPGLYGLYFC221 - 231222 - 232
14ASPASPGLYGLYDB221 - 231222 - 232
24ASPASPGLYGLYZE221 - 231222 - 232

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999566, 0.004473, -0.029106), (-0.006917, 0.925079, 0.379712), (0.028624, 0.379748, -0.924647)-34.99912, 6.35817, -24.62289
2given(-0.998958, 0.033076, -0.031438), (0.012472, 0.860589, 0.509148), (0.043895, 0.508225, -0.860105)-34.62398, 4.22588, -23.98873
3given(-0.996873, 0.045714, 0.064448), (0.072349, 0.855987, 0.511911), (-0.031765, 0.514973, -0.856618)-32.2072, 11.56417, -23.61895
4given(-0.99606, -0.071507, -0.052459), (-0.0868, 0.907372, 0.411268), (0.018192, 0.414201, -0.910004)-37.33685, 3.92409, -23.55891

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Components

#1: Protein
NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / PROTEIN N


Mass: 26620.275 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LA CROSSE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04873
#2: RNA chain POLY-URIDINE 45-MER


Mass: 13732.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
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: 2.78 Å3/Da / Density % sol: 55.8 % / Description: NONE
Crystal growpH: 9
Details: 0.1 M BICINE PH 9 AND 10% PEG 5K MME PROTEIN:RNA RATIO 4:1.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 18433 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.89
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.89 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BGP

4bgp


Resolution: 3.4→44.35 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / SU B: 33.466 / SU ML: 0.502 / Cross valid method: THROUGHOUT / ESU R Free: 0.621 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25213 867 5.1 %RANDOM
Rwork0.19827 ---
obs0.20098 16130 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.212 Å2
Baniso -1Baniso -2Baniso -3
1--8.05 Å20 Å21.55 Å2
2---5.29 Å20 Å2
3---10.93 Å2
Refinement stepCycle: LAST / Resolution: 3.4→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7282 877 0 0 8159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198424
X-RAY DIFFRACTIONr_bond_other_d0.0040.027485
X-RAY DIFFRACTIONr_angle_refined_deg1.121.86711564
X-RAY DIFFRACTIONr_angle_other_deg0.864317293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06524.239368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.572151283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8481544
X-RAY DIFFRACTIONr_chiral_restr0.0670.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021959
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B30808.64
12F30808.64
21D30809.4
22Z30809.4
31B17510.91
32F17510.91
41D17521.7
42Z17521.7
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 63 -
Rwork0.324 1197 -
obs--99.76 %

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