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- PDB-5h5n: The crystal structure of the NS1 (H17N10) RNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 5h5n
TitleThe crystal structure of the NS1 (H17N10) RNA-binding domain
ComponentsNon-structural protein 1
KeywordsRNA BINDING PROTEIN / influenza virus / RNA-binding domain
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / : / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host gene expression / host cell nucleus / RNA binding
Similarity search - Function
Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding / Helix Hairpins / S15/NS1, RNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhao, X. / Qi, J. / Xiao, H. / Gao, G.F.
CitationJournal: J.Gen.Virol. / Year: 2016
Title: The NS1 gene from bat-derived influenza-like virus H17N10 can be rescued in influenza A PR8 backbone
Authors: Zhao, X. / Tefsen, B. / Li, Y. / Qi, J. / Lu, G. / Shi, Y. / Yan, J. / Xiao, H. / Gao, G.F.
History
DepositionNov 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)17,1382
Polymers17,1382
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-15 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.847, 53.847, 114.927
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 Non-structural protein 1 / NS1


Mass: 8568.854 Da / Num. of mol.: 2 / Fragment: UNP residues 1-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)
Gene: NS1, NS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H6QM99
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.085M HEPES pH 7.5, 3.655M sodium chloride, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 11847 / % possible obs: 97.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AIL

1ail


Resolution: 2→39.292 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.253 565 4.78 %
Rwork0.2096 --
obs0.2116 11821 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 70 1218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091177
X-RAY DIFFRACTIONf_angle_d1.2451583
X-RAY DIFFRACTIONf_dihedral_angle_d14.706459
X-RAY DIFFRACTIONf_chiral_restr0.087173
X-RAY DIFFRACTIONf_plane_restr0.006202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.20040.27821470.21672737X-RAY DIFFRACTION99
2.2004-2.51880.29671260.20022818X-RAY DIFFRACTION99
2.5188-3.17320.24681470.22322860X-RAY DIFFRACTION100
3.1732-39.29950.2421450.20492841X-RAY DIFFRACTION94
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)
10.2864-0.0360.1360.10440.12160.2644-0.00210.0965-0.0572-0.0722-0.2167-0.23940.21380.00800.47140.01120.01490.43320.02620.39811.652211.9012-19.8208
20.08920.097-0.01720.4175-0.14830.3818-0.05310.2230.0728-0.3020.0697-0.0148-0.007-0.046200.44090.01250.00320.45580.04240.42553.957214.2519-22.3244
30.2898-0.1732-0.18690.15690.1830.19720.1748-0.13010.29610.2019-0.17840.3282-0.272-0.084900.41490.01270.02940.45390.02670.46080.581525.8779-15.0235
40.1426-0.0139-0.08210.20620.12980.09810.0418-0.18720.01750.2293-0.02590.05680.01710.152-00.4734-0.00310.06120.461-0.00020.47566.648519.2591-7.7519
50.18590.0501-0.06760.0615-0.06230.06830.0443-0.52150.1744-0.01060.12180.5462-0.3716-0.6644-00.44280.103-0.01120.51210.0410.6838-5.439728.539-16.9677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 72 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 25 )
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 51 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 72 )

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