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- PDB-4uc9: N-terminal globular domain of the RSV Nucleoprotein in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4uc9
TitleN-terminal globular domain of the RSV Nucleoprotein in complex with C- terminal dipeptide of the Phosphoprotein
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
ASPARTIC ACID / PHENYLALANINE / Nucleoprotein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: NUCLEOPROTEIN
D: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,93119
Polymers105,0654
Non-polymers1,86615
Water9,746541
1
A: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6614
Polymers26,2661
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7575
Polymers26,2661
Non-polymers4904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8536
Polymers26,2661
Non-polymers5865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6614
Polymers26,2661
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.510, 72.510, 383.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
NUCLEOPROTEIN / PROTEIN N / NUCLEOCAPSID PROTEIN


Mass: 26266.316 Da / Num. of mol.: 4 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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 DIPEPTIDE 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: 2.47 Å3/Da / Density % sol: 50.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 39937 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 43.02 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.9 / % possible all: 74.6

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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: 2.4→14.87 Å / Cor.coef. Fo:Fc: 0.8231 / Cor.coef. Fo:Fc free: 0.7837 / SU R Cruickshank DPI: 0.418 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.526 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.265
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1992 5.03 %RANDOM
Rwork0.1942 ---
obs0.197 39586 95.86 %-
Displacement parametersBiso mean: 48.99 Å2
Baniso -1Baniso -2Baniso -3
1-17.5055 Å20 Å20 Å2
2--17.5055 Å20 Å2
3----35.011 Å2
Refine analyzeLuzzati coordinate error obs: 0.333 Å
Refinement stepCycle: LAST / Resolution: 2.4→14.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6834 0 112 541 7487
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017080HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089520HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2540SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1024HARMONIC5
X-RAY DIFFRACTIONt_it7080HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion19.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion941SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8093SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3041 105 5.24 %
Rwork0.2424 1898 -
all0.2457 2003 -
obs--95.86 %
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)
12.1397-0.04750.13492.05420.06951.9843-0.0371-0.073-0.12730.16490.0530.12360.1146-0.0823-0.0159-0.0790.04440.01580.00720.029-0.4463-16.279531.2128-10.9316
22.3552-0.39840.06632.17840.36012.3174-0.1112-0.11330.06130.13630.0767-0.1076-0.27410.00290.0346-0.0410.0222-0.02280.003-0.0102-0.462615.5139.5283-25.5516
33.17880.6992-0.04991.4531-0.24562.4785-0.0504-0.03770.0511-0.015-0.0497-0.0556-0.03530.20210.1001-0.10360.0142-0.0078-0.02760.0041-0.437617.529946.9418-29.1912
44.5462-0.40851.29221.2584-0.22043.4948-0.0250.1628-0.3152-0.0169-0.028-0.01620.21820.10110.053-0.080.0199-0.0181-0.02670.002-0.4312-18.323929.2102-52.09
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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