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- PDB-3pmk: Crystal structure of the Vesicular Stomatitis Virus RNA free nucl... -

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Basic information

Entry
Database: PDB / ID: 3pmk
TitleCrystal structure of the Vesicular Stomatitis Virus RNA free nucleoprotein/phosphoprotein complex
Components
  • Nucleocapsid proteinVirus
  • Phosphoprotein
KeywordsVIRAL PROTEIN / chaperone
Function / homology
Function and homology information


virion component => GO:0044423 / helical viral capsid / viral nucleocapsid / host cell cytoplasm / RNA-dependent RNA polymerase activity / RNA binding / cytoplasm
Similarity search - Function
Phosphoprotein, central domain / Phosphoprotein, C-terminal domain, viral / 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 ...Phosphoprotein, central domain / Phosphoprotein, C-terminal domain, viral / 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
Nucleocapsid protein / Phosphoprotein
Similarity search - Component
Biological speciesRecombinant vesicular stomatitis Indiana virus rVSV-G/GFP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsLeyrat, C. / Yabukarski, F. / Tarbouriech, N. / Ruigrok, R.W.H. / Jamin, M.
CitationJournal: Plos Pathog. / Year: 2011
Title: Structure of the Vesicular Stomatitis Virus N0-P Complex
Authors: Leyrat, C. / Yabukarski, F. / Tarbouriech, N. / Ribeiro, E.A. / Jensen, M.R. / Blackledge, M. / Ruigrok, R.W. / Jamin, M.
History
DepositionNov 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein
N: Phosphoprotein
O: Phosphoprotein
P: Phosphoprotein
Q: Phosphoprotein
R: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)267,48610
Polymers267,48610
Non-polymers00
Water5,603311
1
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein
N: Phosphoprotein
O: Phosphoprotein
P: Phosphoprotein
Q: Phosphoprotein
R: Phosphoprotein

A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein
N: Phosphoprotein
O: Phosphoprotein
P: Phosphoprotein
Q: Phosphoprotein
R: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)534,97220
Polymers534,97220
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544x,-y-1,-z-11
Buried area72200 Å2
ΔGint-280 kcal/mol
Surface area175470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.560, 171.970, 239.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 45429.488 Da / Num. of mol.: 5 / Fragment: UNP residues 22-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP
Gene: N, Nucleoprotein / Plasmid: pET-M40 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: B7UCZ2
#2: Protein
Phosphoprotein /


Mass: 8067.667 Da / Num. of mol.: 5 / Fragment: UNP residues 1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP
Gene: P, Phosphoprotein / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: B7UCZ3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4% (w/v) PEG 4000, 0.1M sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.03→59.97 Å / Num. all: 55422 / Num. obs: 54333 / % possible obs: 89.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 47.521 Å2 / Rsym value: 0.114 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.03-3.2180.7
3.2-3.39182.7
3.39-3.63184.4
3.63-3.92188.2
3.92-4.29192.2
4.29-4.8196.4
4.8-5.54198.4
5.54-6.78199.1
6.78-9.591100
9.59-59.97199.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIC chain E

2gic


Resolution: 3.03→59.97 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.804 / SU B: 47.3 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27791 2742 5.1 %RANDOM
Rwork0.2439 ---
obs0.24561 51301 89.04 %-
all-55422 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.996 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2--0.95 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 3.03→59.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17167 0 0 311 17478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02217542
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.96423704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3652157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61324.074810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.407153069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.92915110
X-RAY DIFFRACTIONr_chiral_restr0.0630.22544
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02113317
X-RAY DIFFRACTIONr_mcbond_it0.1571.510751
X-RAY DIFFRACTIONr_mcangle_it0.284217275
X-RAY DIFFRACTIONr_scbond_it0.14936791
X-RAY DIFFRACTIONr_scangle_it0.2694.56429
LS refinement shellResolution: 3.034→3.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 202 -
Rwork0.302 3303 -
obs--79.07 %
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)
11.2599-0.17590.33220.4518-0.04220.6627-0.0215-0.02080.0367-0.00530.02160.0470.0461-0.039900.1189-0.01990.02190.1410.01810.082-15.3996-66.1113-167.7795
21.3798-0.4069-0.2880.51440.16180.5593-0.0335-0.0452-0.05180.02180.00520.0766-0.0165-0.07120.02820.1566-0.0143-0.01340.1668-0.00130.1008-15.3137-73.9127-69.4837
31.2941-0.5893-0.39690.57360.17870.6957-0.03020.01790.0131-0.03130.00390.04070.0044-0.04180.02630.1012-0.0334-0.02560.0977-0.01310.0941-15.4907-46.5143-86.3173
41.4132-0.36440.38160.5859-0.0760.8878-0.0153-0.07610.0572-0.01760.02840.08460.0166-0.117-0.01310.1399-0.02110.01940.13850.00960.115-15.3165-41.5716-147.0347
51.4885-0.48630.04750.52530.03910.7871-0.0245-0.0580.0383-0.03560.03240.053-0.0035-0.1425-0.00790.116-0.02370.00640.18150.01830.1154-15.3814-34.0332-115.7518
63.9125-1.7403-1.43912.73080.73964.356-0.0134-0.02660.41990.07470.1667-0.1741-0.1275-0.3327-0.15330.14570.0748-0.09330.15010.03190.169-5.7294-30.7816-114.348
73.7966-2.2654-3.69256.6443-0.25077.34390.2268-0.14190.20860.2249-0.2815-0.37150.02260.26070.05470.1066-0.0257-0.00620.16320.06340.1323-4.505-37.5358-148.6858
89.43613.4048-0.45542.6862-0.47044.4099-0.1173-0.9082-0.308-0.3798-0.25620.08990.0738-0.09850.37350.14970.0811-0.0450.19680.01840.0794-5.439-74.3131-65.533
94.05531.2336-1.11725.3891.0635.0885-0.1969-0.2250.1622-0.10590.07610.06190.09960.74140.12080.07060.0326-0.00390.2910.05670.0458-4.8047-44.2579-84.1737
107.1637-2.3553-3.60444.4861-1.85166.8207-0.30590.19380.13950.09990.0015-0.0130.355-0.34770.30450.1021-0.0662-0.02380.12350.00710.0974-5.3686-63.5731-170.682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 422
2X-RAY DIFFRACTION2B19 - 422
3X-RAY DIFFRACTION3C19 - 422
4X-RAY DIFFRACTION4D19 - 422
5X-RAY DIFFRACTION5E19 - 422
6X-RAY DIFFRACTION6N6 - 35
7X-RAY DIFFRACTION7O5 - 33
8X-RAY DIFFRACTION8P6 - 34
9X-RAY DIFFRACTION9Q5 - 34
10X-RAY DIFFRACTION10R6 - 34

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