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- PDB-6j1u: influenza virus nucleoprotein with a specific inhibitor -

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Basic information

Entry
Database: PDB / ID: 6j1u
Titleinfluenza virus nucleoprotein with a specific inhibitor
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / inhibitor / complex / influenza / H1N1
Function / homology
Function and homology information


negative stranded viral RNA replication / helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Chem-B7O / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPang, B. / Zhang, W.Z. / Zhang, H.M. / Hao, Q.
CitationJournal: J.Virol. / Year: 2021
Title: Discovery of a Novel Specific Inhibitor Targeting Influenza A Virus Nucleoprotein with Pleiotropic Inhibitory Effects on Various Steps of the Viral Life Cycle.
Authors: Yang, F. / Pang, B. / Lai, K.K. / Cheung, N.N. / Dai, J. / Zhang, W. / Zhang, J. / Chan, K.H. / Chen, H. / Sze, K.H. / Zhang, H. / Hao, Q. / Yang, D. / Yuen, K.Y. / Kao, R.Y.
History
DepositionDec 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,6566
Polymers169,3643
Non-polymers1,2913
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.592, 126.747, 194.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A20 - 489
2114B20 - 489
3114C20 - 489

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.802519, -0.125006, 0.583384), (0.465366, -0.480741, -0.743183), (0.373359, 0.867906, -0.32763)-29.68191, -26.46957, 86.61993
3given(0.978098, 0.113614, 0.1744), (-0.10143, -0.471498, 0.876015), (0.181757, -0.874518, -0.449647)-8.29643, -90.70024, 10.07898

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Components

#1: Protein Nucleoprotein


Mass: 56454.793 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1)
Strain: A/Wilson-Smith/1933 H1N1 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q1K9H2, UniProt: P15682*PLUS
#2: Chemical ChemComp-B7O / ~{N}-[4-[(4-~{tert}-butylphenyl)carbonylamino]phenyl]-2,3-dihydro-1,4-benzodioxine-6-carboxamide


Mass: 430.496 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H26N2O4

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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: 43.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium acetate, 0.05 M magnesium acetate, 0.1 M MES, pH 6.0, 7% PEG8000 and 5% glycerol
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 39939 / % possible obs: 92.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.118 / Net I/av σ(I): 13.9 / Net I/σ(I): 13.9
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3247 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IQH

2iqh


Resolution: 2.8→43.53 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.877 / SU B: 31.451 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25971 1810 5.1 %RANDOM
Rwork0.19139 ---
obs0.19499 33729 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.282 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å2-0 Å2
2---0.47 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.8→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10343 0 96 0 10439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01410622
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179347
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.67314297
X-RAY DIFFRACTIONr_angle_other_deg1.5391.64221944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00251303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70919.64639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.538151870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.40715135
X-RAY DIFFRACTIONr_chiral_restr0.0790.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212134
X-RAY DIFFRACTIONr_gen_planes_other0.010.021978
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.154.6675251
X-RAY DIFFRACTIONr_mcbond_other3.1484.6675250
X-RAY DIFFRACTIONr_mcangle_it5.0846.9946541
X-RAY DIFFRACTIONr_mcangle_other5.0836.9946542
X-RAY DIFFRACTIONr_scbond_it3.5325.165369
X-RAY DIFFRACTIONr_scbond_other3.5325.1615370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7557.5927756
X-RAY DIFFRACTIONr_long_range_B_refined8.67553.58911808
X-RAY DIFFRACTIONr_long_range_B_other8.67553.59111809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 6405 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional1.410.5
Amedium positional1.580.5
Amedium positional2.410.5
Bmedium thermal8.312
Bmedium thermal8.622
Bmedium thermal13.852
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 107 -
Rwork0.235 2286 -
obs--89.09 %
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)
10.18680.03980.07040.06710.04120.3045-0.01130.00960.01530.02230.05440.02860.03210.0062-0.04310.01360.01930.00460.05030.01620.0966-27.3483-38.613359.9507
20.20930.0049-0.11710.20540.03940.07530.02550.04710.0480.00140.00660.0029-0.0105-0.0291-0.03210.0174-0.0231-0.01380.0890.03740.0556-13.6931-17.289319.1377
30.4463-0.03570.01570.11380.14190.2057-0.05450.148-0.0934-0.00480.06110.029-0.02910.1144-0.00660.0197-0.03820.03290.1186-0.03990.0705-14.9986-70.727519.659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 489
2X-RAY DIFFRACTION2B22 - 490
3X-RAY DIFFRACTION3C21 - 490

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