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

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Basic information

Entry
Database: PDB / ID: 4uca
TitleN-terminal globular domain of the RSV Nucleoprotein in complex with C- terminal peptide of the Phosphoprotein
Components
  • NUCLEOPROTEIN
  • PHOSPHOSPROTEIN
KeywordsVIRAL PROTEIN / RIBONUCLEOPROTEIN / NUCLEOCAPSID / PHOSPHOPROTEIN / ANTIVIRAL COMPOUNDS / HALOGEN BOND
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / helical viral capsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / viral life cycle / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / PKR-mediated signaling / : / viral nucleocapsid ...symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / helical viral capsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / viral life cycle / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / PKR-mediated signaling / : / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA-dependent RNA polymerase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA binding
Similarity search - Function
Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
Nucleoprotein / Phosphoprotein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 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
C: PHOSPHOSPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2306
Polymers52,9423
Non-polymers2883
Water905
1
A: NUCLEOPROTEIN
C: PHOSPHOSPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8684
Polymers26,6762
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3622
Polymers26,2661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.840, 71.580, 177.200
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: 26266.316 Da / Num. of mol.: 2 / Fragment: N-TERMINAL GLOBULAR DOMAIN, UNP 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: Protein/peptide PHOSPHOSPROTEIN


Mass: 409.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN RESPIRATORY SYNCYTIAL VIRUS A2 / References: UniProt: P03421*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL MGS- AND C-TERMINAL -LEHHHHHH AMINO ACIDS COMES FROM CLONING ASP A300 PHE A301 ...N-TERMINAL MGS- AND C-TERMINAL -LEHHHHHH AMINO ACIDS COMES FROM CLONING ASP A300 PHE A301 CORRESPONDS TO THE C-TERMINAL PEPTIDE OF THE RSV PHOSPHOPROTEIN 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: 2.1 Å3/Da / Density % sol: 41.54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.22→45 Å / Num. obs: 7219 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 62.47 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.7
Reflection shellResolution: 3.22→3.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / % possible all: 86

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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
Resolution: 3.22→20 Å / Cor.coef. Fo:Fc: 0.9184 / Cor.coef. Fo:Fc free: 0.8784 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.52
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 707 9.86 %RANDOM
Rwork0.1918 ---
obs0.1955 7170 95.93 %-
Displacement parametersBiso mean: 68.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.0177 Å20 Å20 Å2
2--6.1909 Å20 Å2
3---0.8268 Å2
Refine analyzeLuzzati coordinate error obs: 0.659 Å
Refinement stepCycle: LAST / Resolution: 3.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 15 5 3473
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013531HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084746HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1273SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes510HARMONIC5
X-RAY DIFFRACTIONt_it3531HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion18.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion469SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4065SEMIHARMONIC4
LS refinement shellResolution: 3.22→3.6 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2763 179 9.54 %
Rwork0.2294 1697 -
all0.2337 1876 -
obs--95.93 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.168-0.0932-0.56912.67840.30384.46680.1615-0.08910.0060.1348-0.2927-0.2847-0.25280.09710.1312-0.3029-0.0197-0.0083-0.32260.1167-0.2389-10.503910.2101-32.6984
23.1246-2.1606-0.04065.5439-0.12634.0608-0.1646-0.21670.18240.82710.00570.1874-0.142-0.39910.159-0.0363-0.15470.135-0.2496-0.115-0.20645.176142.7898-16.0142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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