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- PDB-7dkg: Influenza H5N1 nucleoprotein (truncated) in complex with nucleotides -

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Basic information

Entry
Database: PDB / ID: 7dkg
TitleInfluenza H5N1 nucleoprotein (truncated) in complex with nucleotides
Components
  • Nucleoprotein
  • RNA (5'-R(P*(OMU)P*(OMU)P*(OMU))-3')
KeywordsVIRAL PROTEIN/RNA / nucleocapsid / RNA-binding / influenza / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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
DepositionNov 24, 2020Deposition 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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))-3')


Theoretical massNumber of molelcules
Total (without water)116,5463
Polymers116,5463
Non-polymers00
Water88349
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)53.810, 60.120, 81.370
Angle α, β, γ (deg.)107.31, 106.68, 96.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 23 - 496 / Label seq-ID: 59 - 505

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 57014.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Chicken/Hong Kong/786/97 (H5N1))
Strain: A/Chicken/Hong Kong/786/97 (H5N1) / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PX50
#2: DNA chain RNA (5'-R(P*(OMU)P*(OMU)P*(OMU))-3')


Mass: 2516.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5 and 5% propan-2-ol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→38.58 Å / Num. obs: 15710 / % possible obs: 86.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.171 / Num. unique obs: 2610 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: An in-house model not deposited

Resolution: 3→36.61 Å / Cor.coef. Fo:Fc: 0.75 / Cor.coef. Fo:Fc free: 0.686 / SU B: 24.332 / SU ML: 0.449 / Cross valid method: THROUGHOUT / ESU R Free: 0.699 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33167 803 5.1 %RANDOM
Rwork0.28861 ---
obs0.29085 14906 86.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å21.97 Å2-1.87 Å2
2--0.81 Å2-1.22 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 3→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 63 0 49 6421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136469
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176085
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.668692
X-RAY DIFFRACTIONr_angle_other_deg1.361.58714020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.38119.821390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.473151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.841582
X-RAY DIFFRACTIONr_chiral_restr0.0610.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027227
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021487
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_it1.7953.323196
X-RAY DIFFRACTIONr_mcbond_other1.7963.323195
X-RAY DIFFRACTIONr_mcangle_it3.0774.9623974
X-RAY DIFFRACTIONr_mcangle_other3.0764.9623975
X-RAY DIFFRACTIONr_scbond_it1.7383.5363273
X-RAY DIFFRACTIONr_scbond_other1.7373.5363271
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0415.2214719
X-RAY DIFFRACTIONr_long_range_B_refined7.36460.39526953
X-RAY DIFFRACTIONr_long_range_B_other7.36360.39926952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11545 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 59 -
Rwork0.258 1099 -
obs--88.4 %

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