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- PDB-3pu4: Crystal Structure of a vesicular stomatitis virus nucleocapsid-po... -

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Basic information

Entry
Database: PDB / ID: 3pu4
TitleCrystal Structure of a vesicular stomatitis virus nucleocapsid-polyU 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 / Nucleoprotein / Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / 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 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 / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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 / _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)255,79726
Polymers250,3966
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)511,59452
Polymers500,79212
Non-polymers10,80140
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area83920 Å2
ΔGint-635 kcal/mol
Surface area173310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.477, 235.065, 75.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROchain A and (resseq 2:357 or resseq 366:422 )AA2 - 3571 - 356
12THRTHRLYSLYSchain A and (resseq 2:357 or resseq 366:422 )AA366 - 422365 - 421
21SERSERPROPROchain B and (resseq 2:357 or resseq 366:422 )BB2 - 3571 - 356
22THRTHRLYSLYSchain B and (resseq 2:357 or resseq 366:422 )BB366 - 422365 - 421
31SERSERPROPROchain C and (resseq 2:357 or resseq 366:422 )CC2 - 3571 - 356
32THRTHRLYSLYSchain C and (resseq 2:357 or resseq 366:422 )CC366 - 422365 - 421
41SERSERPROPROchain D and (resseq 2:357 or resseq 366:422 )DD2 - 3571 - 356
42THRTHRLYSLYSchain D and (resseq 2:357 or resseq 366:422 )DD366 - 422365 - 421
51SERSERPROPROchain E and (resseq 2:357 or resseq 366:422 )EE2 - 3571 - 356
52THRTHRLYSLYSchain E and (resseq 2:357 or resseq 366:422 )EE366 - 422365 - 421

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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: 13732.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Midland Reagent Company / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: BL9-2 / Wavelength: 0.97917 Å
DetectorType: MAR 325 CCD / Date: Apr 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. all: 51903 / Num. obs: 51903 / % possible obs: 86.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 77.39 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.311 / % possible all: 45.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→34.774 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2883 1834 3.69 %RANDOM
Rwork0.2506 ---
all0.2519 49700 --
obs0.2519 49700 83.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.618 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 272.56 Å2 / Biso mean: 88.2195 Å2 / Biso min: 44.06 Å2
Baniso -1Baniso -2Baniso -3
1-29.649 Å2-0 Å2-0 Å2
2---3.4078 Å20 Å2
3----26.2412 Å2
Refinement stepCycle: LAST / Resolution: 3→34.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16517 900 20 0 17437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01117883
X-RAY DIFFRACTIONf_angle_d1.39224402
X-RAY DIFFRACTIONf_chiral_restr0.0922716
X-RAY DIFFRACTIONf_plane_restr0.0052984
X-RAY DIFFRACTIONf_dihedral_angle_d21.1526706
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3275X-RAY DIFFRACTIONPOSITIONAL0.047
12B3275X-RAY DIFFRACTIONPOSITIONAL0.047
13C3275X-RAY DIFFRACTIONPOSITIONAL0.045
14D3275X-RAY DIFFRACTIONPOSITIONAL0.053
15E3275X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.08110.4239620.34461568163036
3.0811-3.17170.4177840.30772217230151
3.1717-3.2740.29591150.28832938305367
3.274-3.39090.31981310.29623444357579
3.3909-3.52650.31421410.27473674381584
3.5265-3.68690.30141470.25543845399287
3.6869-3.8810.27631490.25273956410590
3.881-4.12380.29271550.25144064421992
4.1238-4.44160.27311610.23054250441195
4.4416-4.88750.26761680.22244352452099
4.8875-5.59220.25051710.2184428459999
5.5922-7.0360.27751700.2364490466099
7.036-34.77660.27811800.24124640482098

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