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- PDB-3pu1: Crystal Structure of a vesicular stomatitis virus nucleocapsid-po... -

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Basic information

Entry
Database: PDB / ID: 3pu1
TitleCrystal Structure of a vesicular stomatitis virus nucleocapsid-polyG complex
Components
  • Nucleoprotein
  • RNA (45-MER)
KeywordsVIRAL PROTEIN/RNA / RNA / nucleocapsid / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URANYL (VI) ION / RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.14 Å
AuthorsLuo, M. / Green, T.J. / Rowse, M.
CitationJournal: J.Virol. / Year: 2011
Title: Access to RNA Encapsidated in the Nucleocapsid of Vesicular Stomatitis Virus.
Authors: Green, T.J. / Rowse, M. / Tsao, J. / Kang, J. / Ge, P. / Zhou, Z.H. / Luo, M.
History
DepositionDec 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Apr 11, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / pdbx_entity_src_syn
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
R: RNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,55426
Polymers252,1536
Non-polymers5,40120
Water00
1
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
R: RNA (45-MER)
hetero molecules

A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
R: RNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,10752
Polymers504,30612
Non-polymers10,80140
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area85700 Å2
ΔGint-605 kcal/mol
Surface area170440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.222, 233.189, 75.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:165 or resseq 171: 358 or resseq 366:422 )
211chain B and (resseq 2:165 or resseq 171: 358 or resseq 366:422 )
311chain C and (resseq 2:165 or resseq 171: 358 or resseq 366:422 )
411chain D and (resseq 2:165 or resseq 171: 358 or resseq 366:422 )
511chain E and (resseq 2:165 or resseq 171: 358 or resseq 366:422 )

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Components

#1: Protein
Nucleoprotein / NP / Nucleocapsid protein / Protein N


Mass: 47332.750 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Gene: N / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03521
#2: RNA chain RNA (45-MER)


Mass: 15489.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: O2U
Nonpolymer detailsThe IUM REPRESENT URNAYL (IV) IONS [UO2]2+ EVEN THOUGH THE OXYGEN ATOMS COULD NOT BE ACCURATELY ...The IUM REPRESENT URNAYL (IV) IONS [UO2]2+ EVEN THOUGH THE OXYGEN ATOMS COULD NOT BE ACCURATELY PLACED DUE TO LOW RESOLUTION OF THE STRUCTURE.

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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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 5.5 % PEG 3350, 200 mM sodium chloride, 100mM sodium acetate, pH 4.5, vapor diffusion, hanging drop, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98008 Å
DetectorType: MAR 325 CCD / Date: Jan 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 3.14→45.1 Å / Num. obs: 42182 / % possible obs: 82.6 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 76.24 Å2 / Rmerge(I) obs: 0.094
Reflection shellResolution: 3.14→3.26 Å / % possible all: 64.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→45.1 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.41 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.305 1911 4.73 %
Rwork0.259 --
obs0.261 40440 79 %
all-40440 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.73 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 97.18 Å2
Baniso -1Baniso -2Baniso -3
1-35.1875 Å2-0 Å2-0 Å2
2---6.8535 Å20 Å2
3----28.334 Å2
Refinement stepCycle: LAST / Resolution: 3.14→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16517 1035 20 0 17572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118063
X-RAY DIFFRACTIONf_angle_d1.35424717
X-RAY DIFFRACTIONf_dihedral_angle_d18.8466811
X-RAY DIFFRACTIONf_chiral_restr0.0932716
X-RAY DIFFRACTIONf_plane_restr0.0052984
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3241X-RAY DIFFRACTIONPOSITIONAL
12B3241X-RAY DIFFRACTIONPOSITIONAL0.049
13C3233X-RAY DIFFRACTIONPOSITIONAL0.046
14D3241X-RAY DIFFRACTIONPOSITIONAL0.058
15E3241X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1416-3.22010.3826900.34761835X-RAY DIFFRACTION54
3.2201-3.30720.4174990.3251931X-RAY DIFFRACTION56
3.3072-3.40440.3015980.30791989X-RAY DIFFRACTION58
3.4044-3.51430.36411070.28132110X-RAY DIFFRACTION62
3.5143-3.63980.26351070.26492266X-RAY DIFFRACTION65
3.6398-3.78550.31821200.26792404X-RAY DIFFRACTION70
3.7855-3.95770.29711170.25392530X-RAY DIFFRACTION73
3.9577-4.16620.27081380.24542762X-RAY DIFFRACTION80
4.1662-4.4270.26981560.24023103X-RAY DIFFRACTION90
4.427-4.76850.26231710.21613384X-RAY DIFFRACTION97
4.7685-5.24770.27831710.22423448X-RAY DIFFRACTION99
5.2477-6.00560.2831770.24343505X-RAY DIFFRACTION99
6.0056-7.56060.28731760.24983552X-RAY DIFFRACTION100
7.5606-45.14510.35351840.27013710X-RAY DIFFRACTION100

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