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- PDB-4co6: Crystal structure of the Nipah virus RNA free nucleoprotein- phos... -

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Basic information

Entry
Database: PDB / ID: 4co6
TitleCrystal structure of the Nipah virus RNA free nucleoprotein- phosphoprotein complex
Components
  • NUCLEOPROTEIN
  • PHOSPHOPROTEIN
KeywordsCHAPERONE / VIRAL PROTEIN / VIRAL REPLICATION / PARAMYXOVIRUS
Function / homology
Function and homology information


negative stranded viral RNA transcription / negative stranded viral RNA replication / helical viral capsid / virus-mediated perturbation of host defense response / virion component / viral nucleocapsid / host cell cytoplasm / molecular adaptor activity / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2490 / Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Paramyxovirus nucleocapsid protein ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2490 / Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
BROMIDE ION / Phosphoprotein / Nucleoprotein
Similarity search - Component
Biological speciesNIPAH VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.498 Å
AuthorsYabukarksi, F. / Lawrence, P. / Tarbouriech, N. / Bourhis, J.M. / Jensen, M.R. / Ruigrok, R.W.H. / Blackledge, M. / Volchkov, V. / Jamin, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structure of Nipah Virus Unassembled Nucleoprotein in Complex with its Viral Chaperone.
Authors: Yabukarksi, F. / Lawrence, P. / Tarbouriech, N. / Bourhis, J.M. / Delaforge, E. / Jensen, M.R. / Ruigrok, R.W.H. / Blackledge, M. / Volchkov, V. / Jamin, M.
History
DepositionJan 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: PHOSPHOPROTEIN
E: PHOSPHOPROTEIN
F: PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,79015
Polymers139,3826
Non-polymers4089
Water1,78399
1
A: NUCLEOPROTEIN
D: PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7188
Polymers46,4612
Non-polymers2576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-61.9 kcal/mol
Surface area18180 Å2
MethodPISA
2
C: NUCLEOPROTEIN
E: PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5413
Polymers46,4612
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-17.8 kcal/mol
Surface area13410 Å2
MethodPISA
3
B: NUCLEOPROTEIN
F: PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5324
Polymers46,4612
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-39.2 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.890, 98.960, 156.910
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 / / PROTEIN N / NUCLEOCAPSID PROTEIN


Mass: 40429.039 Da / Num. of mol.: 3 / Fragment: N0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NIPAH VIRUS / Variant: UMMC1 ISOLATE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9IK92
#2: Protein PHOSPHOPROTEIN / / PROTEIN P


Mass: 6031.779 Da / Num. of mol.: 3 / Fragment: N0 BINDING REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NIPAH VIRUS / Variant: UMMC1 ISOLATE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9IK91
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: MICROSEEDING CONDITIONS 0.2M KBR, 16-20% PEG 3350;

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→49.4 Å / Num. obs: 85866 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 46.94 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.5
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
HKL2MAPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.498→47.189 Å / SU ML: 0.32 / σ(F): 2.03 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 2288 5.1 %
Rwork0.1916 --
obs0.1952 45315 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61 Å2
Refinement stepCycle: LAST / Resolution: 2.498→47.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7532 0 9 99 7640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017663
X-RAY DIFFRACTIONf_angle_d1.15110342
X-RAY DIFFRACTIONf_dihedral_angle_d16.7422863
X-RAY DIFFRACTIONf_chiral_restr0.0441190
X-RAY DIFFRACTIONf_plane_restr0.0051314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4977-2.5520.33441340.24882536X-RAY DIFFRACTION96
2.552-2.61140.28261220.21242693X-RAY DIFFRACTION100
2.6114-2.67670.26591230.2012683X-RAY DIFFRACTION100
2.6767-2.7490.29931430.1932662X-RAY DIFFRACTION100
2.749-2.82990.291430.19262628X-RAY DIFFRACTION100
2.8299-2.92120.2511390.19332666X-RAY DIFFRACTION100
2.9212-3.02560.28491270.19942689X-RAY DIFFRACTION100
3.0256-3.14680.23381590.20312671X-RAY DIFFRACTION100
3.1468-3.28990.27241350.20472682X-RAY DIFFRACTION100
3.2899-3.46330.26141450.19962696X-RAY DIFFRACTION100
3.4633-3.68020.30931410.19062683X-RAY DIFFRACTION100
3.6802-3.96430.27621450.17612701X-RAY DIFFRACTION100
3.9643-4.3630.22821220.16242737X-RAY DIFFRACTION100
4.363-4.99370.21871470.16012723X-RAY DIFFRACTION100
4.9937-6.28920.25681730.20782736X-RAY DIFFRACTION100
6.2892-47.19780.24941900.20742841X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7635-0.20870.14065.03281.256.9978-0.24090.0008-0.18350.25380.07350.14910.3697-0.33190.16920.3289-0.05490.00150.3455-0.09670.323947.87613.610745.9982
22.6309-0.38520.18744.2520.96475.1150.05080.3265-0.0963-0.144-0.0721-0.19910.16870.2569-0.00320.2560.0085-0.02120.28110.00190.226734.612533.938962.8124
33.7754-0.09350.35773.79390.4514.5601-0.0172-0.6885-0.18690.66030.0602-0.18120.53940.0629-0.03620.46740.0013-0.05030.4784-0.01260.300193.4927-22.350645.6344
45.8001-0.93560.74923.95381.49334.64990.09430.4077-0.4251-0.3839-0.02810.05020.2360.1841-0.02710.3958-0.06520.00530.2607-0.01920.235276.9547.459162.1536
52.6109-0.8666-1.06759.16581.10547.01980.22560.16110.4621-0.0565-0.0444-0.2675-0.70990.0999-0.05580.4268-0.03-0.05540.29910.01780.242337.557644.706270.5467
66.9622-0.3709-1.10697.2516-2.2224.8476-0.04410.01650.0309-0.40580.15450.34210.0362-0.955-0.15010.29240.0199-0.06750.6754-0.08050.230267.1336-15.038627.434
78.5827-1.9386-0.32799.72631.41185.55650.30590.13470.6748-0.0129-0.1566-0.3033-1.19650.2938-0.23210.5533-0.09110.01690.28490.06640.206279.827917.894470.2104
84.12630.6912-1.24423.492-0.28812.28170.22930.22330.34680.5045-0.1543-0.1678-0.97921.22670.02810.9703-0.37230.16711.07050.07530.818494.487712.49833.6765
93.4932-0.38180.59373.25680.05233.47530.01280.41640.147-0.5535-0.0794-0.3547-0.34320.45610.08940.36250.00160.02490.48060.02840.300478.1933-12.283818.4453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 32 THROUGH 258 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 259 THROUGH 371 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 32 THROUGH 258 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 259 THROUGH 369)
5X-RAY DIFFRACTION5CHAIN D AND (RESID -1 THROUGH 27 )
6X-RAY DIFFRACTION6CHAIN E AND (RESID -1 THROUGH 36 )
7X-RAY DIFFRACTION7CHAIN F AND (RESID 0 THROUGH 36 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 43 THROUGH 238 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 250 THROUGH 368 )

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