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

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Basic information

Entry
Database: PDB / ID: 4ucc
TitleN-terminal globular domain of the RSV Nucleoprotein in complex with the Nucleoprotein Phosphoprotein interaction inhibitor M76
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 / helical viral capsid / Respiratory syncytial virus genome replication / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / protein serine/threonine kinase inhibitor activity ...Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / helical viral capsid / Respiratory syncytial virus genome replication / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / protein serine/threonine kinase inhibitor activity / 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 / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
Chem-ZKW / Nucleoprotein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)53,1634
Polymers52,5332
Non-polymers6302
Water3,261181
1
A: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5812
Polymers26,2661
Non-polymers3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5812
Polymers26,2661
Non-polymers3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.820, 71.960, 178.170
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: Chemical ChemComp-ZKW / 1-[(2,4-dichlorophenyl)methyl]pyrazole-3,5-dicarboxylic acid


Mass: 315.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H8Cl2N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.19 Å3/Da / Density % sol: 43.77 % / 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: 2.05→45 Å / Num. obs: 28687 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 43.31 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.1
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.1 / % possible all: 90

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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: 2.05→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 2895 10.15 %RANDOM
Rwork0.1914 ---
obs0.1958 28525 98.43 %-
Displacement parametersBiso mean: 66.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.4927 Å20 Å20 Å2
2--2.4542 Å20 Å2
3----0.9615 Å2
Refine analyzeLuzzati coordinate error obs: 0.411 Å
Refinement stepCycle: LAST / Resolution: 2.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 40 181 3736
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013662HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024951HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1316SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes582HARMONIC5
X-RAY DIFFRACTIONt_it3662HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion484SEMIHARMONIC5
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_contact4287SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.13 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2569 287 11.32 %
Rwork0.2338 2248 -
all0.2365 2535 -
obs--98.43 %
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)
12.2338-1.1756-1.07747.18121.98236.77080.3459-0.0309-0.0635-0.8584-0.2883-0.622-0.3055-0.0771-0.0576-0.35280.06330.0638-0.55860.0791-0.4532-10.500210.1576-32.6315
23.1977-1.1115-0.00685.3661-0.39353.3866-0.3596-0.33720.02790.940.3040.42350.1091-0.14410.0556-0.24280.03190.1374-0.49890.0077-0.44765.427342.7393-15.8779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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