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- PDB-4xjn: Structure of the parainfluenza virus 5 nucleocapsid-RNA complex: ... -

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Basic information

Entry
Database: PDB / ID: 4xjn
TitleStructure of the parainfluenza virus 5 nucleocapsid-RNA complex: an insight into paramyxovirus polymerase activity
Components
  • Nucleocapsid
  • RNA (78-MER)
KeywordsVIRAL PROTEIN/RNA / PIV5 / Nucleocapsid / RNA / Complex / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / cytoplasm
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
LEAD (II) ION / RNA / RNA (> 10) / Nucleoprotein / Nucleocapsid
Similarity search - Component
Biological speciesParainfluenza virus 5
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.11 Å
AuthorsAlayyoubi, M. / Leser, G.P. / Kors, C.A. / Lamb, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein-RNA complex.
Authors: Alayyoubi, M. / Leser, G.P. / Kors, C.A. / Lamb, R.A.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_detector.type ..._citation.journal_id_CSD / _diffrn_detector.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.version / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid
B: Nucleocapsid
C: Nucleocapsid
D: Nucleocapsid
E: Nucleocapsid
F: Nucleocapsid
G: Nucleocapsid
H: Nucleocapsid
I: Nucleocapsid
J: Nucleocapsid
K: Nucleocapsid
L: Nucleocapsid
M: Nucleocapsid
N: RNA (78-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)785,92428
Polymers783,02314
Non-polymers2,90114
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area104410 Å2
ΔGint-831 kcal/mol
Surface area183740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.636, 309.436, 233.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H
91chain I
101chain J
111chain K
121chain L
131chain M

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA3 - 401
211chain BB3 - 401
311chain CC3 - 401
411chain DD3 - 401
511chain EE3 - 401
611chain FF3 - 401
711chain GG3 - 401
811chain HH3 - 401
911chain II3 - 401
1011chain JJ3 - 401
1111chain KK3 - 401
1211chain LL3 - 401
1311chain MM3 - 401

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Components

#1: Protein
Nucleocapsid / Nucleocapsid protein


Mass: 58399.004 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parainfluenza virus 5 / Production host: Escherichia coli (E. coli) / References: UniProt: W5QKM4, UniProt: Q88435*PLUS
#2: RNA chain RNA (78-MER)


Mass: 23835.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Pb

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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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystlliztion Condition: 30% PEG 400, 0.1M MES sodium salt pH 6.5, 0.1 M MgCl2. Crystals grew from 4 days to one week, and varied in size from 50um to 400um
PH range: 6.5-7.2 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.95041 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2014
RadiationMonochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95041 Å / Relative weight: 1
ReflectionResolution: 3→171.3 Å / Num. all: 146910 / Num. obs: 132485 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 11.8
Reflection shellResolution: 3→3.05 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.475 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.11→45.007 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 6437 4.87 %
Rwork0.2271 --
obs0.2288 132287 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.05 Å2 / Biso mean: 46.5241 Å2 / Biso min: 15.07 Å2
Refinement stepCycle: final / Resolution: 3.11→45.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40755 1560 14 0 42329
Biso mean--101.81 --
Num. residues----5213
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A24883X-RAY DIFFRACTION11.617TORSIONAL
12B24883X-RAY DIFFRACTION11.617TORSIONAL
13C24883X-RAY DIFFRACTION11.617TORSIONAL
14D24883X-RAY DIFFRACTION11.617TORSIONAL
15E24883X-RAY DIFFRACTION11.617TORSIONAL
16F24883X-RAY DIFFRACTION11.617TORSIONAL
17G24883X-RAY DIFFRACTION11.617TORSIONAL
18H24883X-RAY DIFFRACTION11.617TORSIONAL
19I24883X-RAY DIFFRACTION11.617TORSIONAL
110J24883X-RAY DIFFRACTION11.617TORSIONAL
111K24883X-RAY DIFFRACTION11.617TORSIONAL
112L24883X-RAY DIFFRACTION11.617TORSIONAL
113M24883X-RAY DIFFRACTION11.617TORSIONAL

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