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- PDB-7dxp: Influenza H5N1 nucleoprotein in complex with nucleotides -

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Basic information

Entry
Database: PDB / ID: 7dxp
TitleInfluenza H5N1 nucleoprotein in complex with nucleotides
Components
  • Nucleoprotein
  • RNA (5'-R(P*(OMU)P*(OMU)P*(OMU)P*(OMU))-3')
KeywordsVIRAL PROTEIN/RNA / nucleocapsid / RNA-binding / influenza nucleoprotein / VIRAL PROTEIN-RNA complex
Function / homologyDNA
Function and homology information
Biological speciesInfluenza A virus
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTang, Y.S. / Xu, S. / Chen, Y.W. / Wang, J.H. / Shaw, P.C.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)T11-705/14N Hong Kong
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Crystal structures of influenza nucleoprotein complexed with nucleic acid provide insights into the mechanism of RNA interaction.
Authors: Tang, Y.S. / Xu, S. / Chen, Y.W. / Wang, J.H. / Shaw, P.C.
History
DepositionJan 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: RNA (5'-R(P*(OMU)P*(OMU)P*(OMU)P*(OMU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4485
Polymers117,3243
Non-polymers1242
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Microscale thermophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.010, 60.630, 82.710
Angle α, β, γ (deg.)106.700, 109.010, 96.620
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nucleoprotein /


Mass: 57243.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Hong Kong/483/1997(H5N1))
Strain: A/Hong Kong/483/97(H5N1) / Production host: Escherichia coli (E. coli)
#2: DNA chain RNA (5'-R(P*(OMU)P*(OMU)P*(OMU)P*(OMU))-3')


Mass: 2836.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsMissing residues contain expression tags, disordered residues and a deletion from 402-428.

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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: 1.94 Å3/Da / Density % sol: 36.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 6.0, 0.1 M NaCl and 11% PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→25.52 Å / Num. obs: 37106 / % possible obs: 90.4 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.253 / Num. unique obs: 5475 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.501 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.199 / SU B: 7.704 / SU ML: 0.185 / Average fsc free: 0.8967 / Average fsc work: 0.9135 / Cross valid method: NONE / ESU R: 0.42 / ESU R Free: 0.263
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2484 1866 5.032 %
Rwork0.193 35220 -
all0.196 --
obs-37086 90.33 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.447 Å2
Baniso -1Baniso -2Baniso -3
1-0.848 Å20.252 Å2-0.659 Å2
2--1.025 Å2-0.067 Å2
3----0.864 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6461 66 8 155 6690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136680
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176268
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.6618976
X-RAY DIFFRACTIONr_angle_other_deg1.3271.58814433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.14619.543416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.897151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4641590
X-RAY DIFFRACTIONr_chiral_restr0.0780.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021578
X-RAY DIFFRACTIONr_nbd_refined0.210.21447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.26064
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23234
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0560.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.223
X-RAY DIFFRACTIONr_nbd_other0.2730.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.215
X-RAY DIFFRACTIONr_mcbond_it3.4063.4233272
X-RAY DIFFRACTIONr_mcbond_other3.4043.4223271
X-RAY DIFFRACTIONr_mcangle_it5.1415.114077
X-RAY DIFFRACTIONr_mcangle_other5.1415.1114078
X-RAY DIFFRACTIONr_scbond_it3.8463.9273408
X-RAY DIFFRACTIONr_scbond_other3.8453.9273409
X-RAY DIFFRACTIONr_scangle_it5.9025.7054897
X-RAY DIFFRACTIONr_scangle_other5.9015.7054898
X-RAY DIFFRACTIONr_lrange_it8.39239.5097624
X-RAY DIFFRACTIONr_lrange_other8.39239.5127625
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.0512562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.3590.2811250.23926270.24130060.8250.84891.55020.218
2.359-2.4230.2981280.22825400.23229160.8390.86491.49520.208
2.423-2.4930.2841230.22325110.22528580.8520.88292.16240.199
2.493-2.5690.281390.20824340.21228050.8710.89691.72910.184
2.569-2.6520.2541310.20823120.2126750.8910.89891.32710.188
2.652-2.7440.2451160.20122490.20325980.9010.91591.03160.185
2.744-2.8460.2571150.18621920.18925380.9150.92790.89830.167
2.846-2.9610.2521210.17920670.18324120.9020.92690.71310.164
2.961-3.090.2641010.19419680.19822800.8950.91990.74560.183
3.09-3.2380.2421090.17419200.17822450.9210.94190.37860.168
3.238-3.410.2321070.18818260.19121370.9170.9290.45390.186
3.41-3.6130.2451000.19616930.19920050.9130.92889.42640.196
3.613-3.8560.257730.1815750.18318760.9280.93987.84650.186
3.856-4.1570.221590.17214510.17417600.9370.95185.79550.183
4.157-4.540.201620.16512640.16616120.9450.95682.25810.184
4.54-5.0550.223600.17311570.17614700.9370.9582.78910.2
5.055-5.7960.279670.20811840.21212890.9360.93997.0520.238
5.796-7.0010.247630.20310160.20611140.9220.94796.85820.237
7.001-9.520.23440.1667840.1698770.9380.95894.41280.216
9.52-24.5010.236230.2864500.2835460.9160.92486.630.393

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