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- PDB-4uc8: N-terminal globular domain of the RSV Nucleoprotein in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4uc8
TitleN-terminal globular domain of the RSV Nucleoprotein in complex with C- terminal phenylalanine of the Phosphoprotein
ComponentsNUCLEOPROTEIN
KeywordsVIRAL PROTEIN / RIBONUCLEOPROTEIN / NUCLEOCAPSID / PHOSPHOPROTEIN / ANTIVIRAL COMPOUNDS / HALOGEN BOND
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry ...Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / PKR-mediated signaling / Evasion by RSV of host interferon responses / viral capsid / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
PHENYLALANINE / Nucleoprotein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOuizougun-Oubari, M. / Pereira, N. / Tarus, B. / Galloux, M. / Tortorici, M.-A. / Hoos, S. / Baron, B. / England, P. / Bontems, F. / Rey, F.A. ...Ouizougun-Oubari, M. / Pereira, N. / Tarus, B. / Galloux, M. / Tortorici, M.-A. / Hoos, S. / Baron, B. / England, P. / Bontems, F. / Rey, F.A. / Eleouet, J.-F. / Sizun, C. / Slama-Schwok, A. / Duquerroy, S.
CitationJournal: J.Virol. / Year: 2015
Title: A Druggable Pocket at the Nucleocapsid/Phosphoprotein Interaction Site of the Human Respiratory Syncytial Virus.
Authors: Ouizougun-Oubari, M. / Pereira, N. / Tarus, B. / Galloux, M. / Lassoued, S. / Fix, J. / Tortorici, M.A. / Hoos, S. / Baron, B. / England, P. / Desmaele, D. / Couvreur, P. / Bontems, F. / ...Authors: Ouizougun-Oubari, M. / Pereira, N. / Tarus, B. / Galloux, M. / Lassoued, S. / Fix, J. / Tortorici, M.A. / Hoos, S. / Baron, B. / England, P. / Desmaele, D. / Couvreur, P. / Bontems, F. / Rey, F.A. / Eleouet, J.F. / Sizun, C. / Slama-Schwok, A. / Duquerroy, S.
History
DepositionDec 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,76014
Polymers52,4772
Non-polymers1,28312
Water4,900272
1
B: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0729
Polymers26,2381
Non-polymers8348
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6885
Polymers26,2381
Non-polymers4494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.808, 134.723, 50.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NUCLEOPROTEIN / PROTEIN N / NUCLEOCAPSID PROTEIN


Mass: 26238.303 Da / Num. of mol.: 2 / Fragment: N-TERMINAL GLOBULAR DOMAIN, RESIDUES 31-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS A2 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P03418
#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL MGS- AND C-TERMINAL -LEHHHHHH AMINO ACIDS COMES FROM CLONING. SEQUENCE NUMBERING ...N-TERMINAL MGS- AND C-TERMINAL -LEHHHHHH AMINO ACIDS COMES FROM CLONING. SEQUENCE NUMBERING ACCORDING TO P03418 ENTRY. C-TERMINAL AMNINO-ACID OF THE RSV PHOSPHOPROTEIN. PHE A 301 WAS CO-CRYSTALLIZED WITH THE RSV NUCLEOPROTEIN.

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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: 2.39 Å3/Da / Density % sol: 48.48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 29895 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 29.47 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 61.4

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJ8

2wj8


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.9497 / Cor.coef. Fo:Fc free: 0.9383 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.205 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.159
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1507 5.07 %RANDOM
Rwork0.1779 ---
obs0.1796 29743 88.19 %-
Displacement parametersBiso mean: 39.65 Å2
Baniso -1Baniso -2Baniso -3
1-4.611 Å20 Å20 Å2
2--2.7331 Å20 Å2
3----7.3441 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 76 272 3818
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013651HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14920HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1308SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes531HARMONIC5
X-RAY DIFFRACTIONt_it3651HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion16.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion481SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4361SEMIHARMONIC4
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2193 115 5.74 %
Rwork0.2198 1888 -
all0.2198 2003 -
obs--88.19 %
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)
13.0296-0.9019-0.5772.41480.60141.75260.11130.2349-0.3122-0.1813-0.0630.1926-0.0444-0.0923-0.0483-0.1232-0.0058-0.018-0.1371-0.037-0.110512.217616.51230.0659
21.4685-0.0033-0.1271.4490.43561.3675-0.00310.12710.067-0.0032-0.04280.0465-0.06120.04870.0459-0.1047-0.0035-0.0016-0.12690.0025-0.09879.736648.0621-24.1248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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