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- PDB-5b7b: Crystal structure of Nucleoprotein-nucleozin complex -

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Basic information

Entry
Database: PDB / ID: 5b7b
TitleCrystal structure of Nucleoprotein-nucleozin complex
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / influenza nucleoprotein / nucleozin
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-NUZ / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPang, B. / Zhang, W.Z. / Zhang, H.M. / Hao, Q.
Funding support China, Hong Kong, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370739 China
Research Grants Council of Hong Kong,766412 Hong Kong
Shenzhen governmentZDSYS20140509142721429 China
CitationJournal: Sci Rep / Year: 2016
Title: Structural Characterization of H1N1 Nucleoprotein-Nucleozin Binding Sites
Authors: Pang, B. / Cheung, N.N. / Zhang, W.Z. / Dai, J. / Kao, R.Y. / Zhang, H.M. / Hao, Q.
History
DepositionJun 6, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 6, 2016ID: 4X9A
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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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
E: Nucleoprotein
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,5828
Polymers338,7296
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.021, 121.557, 195.541
Angle α, β, γ (deg.)90.000, 89.790, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13E
23F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 3 / Auth seq-ID: 21 - 489 / Label seq-ID: 21 - 489

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21DD
12BB
22CC
13EE
23FF

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999988, 0.000477, -0.004803), (0.000479, -1, 0.000403), (-0.004803, -0.000406, -0.999988)0.18321, 75.250099, 97.608643
3given(1), (1), (1)
4given(0.999997, 4.9E-5, -0.002566), (4.6E-5, -1, -0.00087), (-0.002566, 0.00087, -0.999996)-0.01392, 75.329033, 97.700737
5given(1), (1), (1)
6given(0.999998, -0.000652, -0.001801), (-0.000653, -1, -0.000254), (-0.0018, 0.000255, -0.999998)-0.06043, 75.226967, 97.650864

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Components

#1: Protein
Nucleoprotein


Mass: 56454.793 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (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-NUZ / [4-(2-chloro-4-nitrophenyl)piperazin-1-yl](5-methyl-3-phenyl-1,2-oxazol-4-yl)methanone / nucleozin


Mass: 426.853 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19ClN4O4

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 6
Details: 0.1 M sodium acetate, 0.05 M magnesium acetate, 0.1 M MES, 7% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 55848 / % possible obs: 92.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.086 / Net I/av σ(I): 16.094 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.113.40.557194.6
3.11-3.233.40.384193.5
3.23-3.383.30.27193.6
3.38-3.563.30.185192.7
3.56-3.783.30.116192.8
3.78-4.073.20.08191.6
4.07-4.483.20.059189.6
4.48-5.133.10.057189.1
5.13-6.463.30.061194.5
6.46-503.20.033190.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IQH

2iqh


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / SU B: 21.35 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.505 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 2824 5.1 %RANDOM
Rwork0.2001 ---
obs0.2032 52949 92.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 189.43 Å2 / Biso mean: 75.76 Å2 / Biso min: 34.83 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å21.51 Å2
2---1.07 Å20 Å2
3----2.3 Å2
Refinement stepCycle: final / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19894 0 60 0 19954
Biso mean--119.43 --
Num. residues----2533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01920274
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.95927263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18452499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17922.104946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.494153635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.27515260
X-RAY DIFFRACTIONr_chiral_restr0.0960.22982
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115289
X-RAY DIFFRACTIONr_mcbond_it4.2557.32310098
X-RAY DIFFRACTIONr_mcangle_it6.89310.9712563
X-RAY DIFFRACTIONr_scbond_it4.6847.71810173
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1614LOOSE POSITIONAL0.025
1A1676TIGHT THERMAL2.70.5
1A1614LOOSE THERMAL2.9710
2B1625LOOSE POSITIONAL0.025
2B1692TIGHT THERMAL2.730.5
2B1625LOOSE THERMAL3.1610
3E1618LOOSE POSITIONAL0.035
3E1684TIGHT THERMAL2.630.5
3E1618LOOSE THERMAL3.2610
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 229 -
Rwork0.3 3912 -
all-4141 -
obs--92.79 %

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