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

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Basic information

Entry
Database: PDB / ID: 4ucd
TitleN-terminal globular domain of the RSV Nucleoprotein in complex with the Nucleoprotein Phosphoprotein interaction inhibitor M81
ComponentsNUCLEOPROTEIN
KeywordsVIRAL PROTEIN / RESPIRATORY SYNCYTIAL VIRUS / RIBONUCLEOPROTEIN / NUCLEOCAPSID / PHOSPHOPROTEIN / ANTIVIRAL COMPOUNDS / HALOGEN BOND
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry ...Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / 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 / symbiont-mediated suppression of host NF-kappaB cascade / 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
Chem-M81 / Nucleoprotein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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)53,1905
Polymers52,5332
Non-polymers6573
Water36020
1
A: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5472
Polymers26,2661
Non-polymers2811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6433
Polymers26,2661
Non-polymers3772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.680, 71.940, 178.550
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, 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-M81 / 1-[(2-chlorophenyl)methyl]pyrazole-3,5-dicarboxylic acid


Mass: 280.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9ClN2O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL MGS- AND C-TERMINAL -LEHHHHHH AMINO ACIDS COMES FROM CLONING

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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: 2.18 Å3/Da / Density % sol: 43.66 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.66→40 Å / Num. obs: 13129 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 69.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 2.66→2.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.8 / % possible all: 81.1

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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: 2.66→20 Å / Cor.coef. Fo:Fc: 0.9576 / Cor.coef. Fo:Fc free: 0.9359 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.299
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 1286 9.86 %RANDOM
Rwork0.174 ---
obs0.178 13043 96.62 %-
Displacement parametersBiso mean: 87.23 Å2
Baniso -1Baniso -2Baniso -3
1--6.285 Å20 Å20 Å2
2--8.5568 Å20 Å2
3----2.2718 Å2
Refine analyzeLuzzati coordinate error obs: 0.412 Å
Refinement stepCycle: LAST / Resolution: 2.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 43 20 3510
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013570HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.044815HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1271SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes561HARMONIC5
X-RAY DIFFRACTIONt_it3570HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion19.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion471SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3868SEMIHARMONIC4
LS refinement shellResolution: 2.66→2.87 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2342 208 9.12 %
Rwork0.2157 2073 -
all0.2173 2281 -
obs--96.62 %
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)
12.9574-0.891-1.2034.92111.60496.54070.2204-0.0396-0.2004-0.2681-0.1472-0.38620.00450.0265-0.0732-0.32170.02810.0207-0.330.0791-0.2348-10.34510.0664-32.5874
25.1839-1.148-0.37546.5534-0.24913.5791-0.3527-0.34010.13791.06330.22960.47590.0975-0.11320.1231-0.2229-0.01350.163-0.3521-0.0028-0.29365.37942.7354-15.8446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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