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- PDB-2z0a: Crystal structure of RNA-binding domain of NS1 from influenza A v... -

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Basic information

Entry
Database: PDB / ID: 2z0a
TitleCrystal structure of RNA-binding domain of NS1 from influenza A virus A/crow/Kyoto/T1/2004(H5N1)
ComponentsNonstructural protein 1
KeywordsVIRAL PROTEIN / avian influenza / H5N1 / RNA-binding / NS1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding / S15/NS1, RNA-binding / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GLYCINE / SUCCINIC ACID / Non-structural protein 1 / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSaijo, S. / Kishishita, S. / Kamo-Uchikubo, T. / Terada, T. / Shirouzu, M. / Ito, H. / Ito, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of RNA-binding domain of NS1 from influenza A virus A/crow/Kyoto/T1/2004(H5N1)
Authors: Saijo, S. / Kishishita, S. / Kamo-Uchikubo, T. / Terada, T. / Shirouzu, M. / Ito, H. / Ito, T. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nonstructural protein 1
B: Nonstructural protein 1
C: Nonstructural protein 1
D: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,91610
Polymers35,3794
Non-polymers5366
Water5,152286
1
A: Nonstructural protein 1
B: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0766
Polymers17,6902
Non-polymers3864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-9 kcal/mol
Surface area8030 Å2
MethodPISA
2
C: Nonstructural protein 1
D: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8404
Polymers17,6902
Non-polymers1502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-16 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.723, 54.378, 66.347
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nonstructural protein 1


Mass: 8844.864 Da / Num. of mol.: 4 / Fragment: RNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: A/crow/Kyoto/T1/2004(H5N1) / Gene: NS1 / Plasmid: PX070216-21 / Production host: Cell-free protein synthesis / References: UniProt: Q5H7I4, UniProt: Q5H7J4*PLUS
#2: Chemical
ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 1.89 Å3/Da / Density % sol: 34.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1M SPG buffer pH 6.8, 25 % (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 13, 2007 / Details: rhodium coated mirror
RadiationMonochromator: fixed exit double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 22185 / % possible obs: 97.8 % / Redundancy: 4 % / Rsym value: 0.066 / Net I/σ(I): 17.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 2033 / Rsym value: 0.274 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AIL

1ail


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.566 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.165 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23828 1132 5.1 %RANDOM
Rwork0.17247 ---
obs0.17584 21044 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.504 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å2-0.57 Å2
2---0.78 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 36 286 2640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212389
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg11.9813199
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5645283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11723.03132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97715450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6841536
X-RAY DIFFRACTIONr_chiral_restr0.0750.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21250
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21664
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4181.51490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.67222300
X-RAY DIFFRACTIONr_scbond_it1.2613996
X-RAY DIFFRACTIONr_scangle_it1.9654.5899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 80 -
Rwork0.21 1416 -
obs-1496 88.31 %
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)
11.93080.62550.79451.80631.12094.75010.0798-0.13-0.09060.0761-0.03350.0534-0.0443-0.2625-0.0463-0.08230.0126-0.0033-0.0849-0.0011-0.04843.55971.413132.7844
211.2547-3.72636.39257.0715-3.34429.9206-0.2053-0.25810.5660.0791-0.0278-0.1624-1.0637-0.22290.23310.01660.02890.0055-0.0734-0.0579-0.02051.799910.7733.114
35.2449-1.22720.504410.4626-1.52183.0020.01350.03760.07360.1071-0.1250.4122-0.1876-0.59450.1115-0.05530.0444-0.02090.026-0.0415-0.0931-3.93381.959724.5579
411.5186-12.36566.192315.7544-6.38196.39880.0901-0.0228-0.17430.24470.07650.06730.0695-0.1475-0.1666-0.0663-0.0430.0029-0.0562-0.0275-0.04836.7607-13.284127.3482
53.42880.6893-0.9432.00471.31273.35090.1222-0.2359-0.10320.16130.0279-0.12510.1154-0.0339-0.1501-0.051-0.0024-0.0226-0.0860.0409-0.030113.6523-1.606837.8212
65.7263-0.00865.485215.6033-1.24099.54450.4140.1832-0.6369-0.6402-0.1466-0.33691.213-0.0118-0.26740.0428-0.01670.0529-0.0304-0.0273-0.008112.0882-4.866619.7942
73.54930.76164.38671.85470.61697.6852-0.07810.0635-0.0806-0.10370.0476-0.2559-0.01340.33220.0305-0.0625-0.00270.0272-0.06860.003-0.030318.86943.966430.884
832.94029.4236-3.90276.0952-0.91693.159-0.0068-0.0354-0.87860.22820.0216-0.24830.3024-0.1136-0.01480.04360.001-0.0066-0.10910.03-0.015710.4437-9.91539.2568
92.3732-0.56322.06771.5786-0.08863.59810.02370.00890.02620.0536-0.0480.0491-0.08380.11820.0243-0.0834-0.03040.0309-0.05130.0102-0.069322.0293-10.42326.1514
1015.2589-0.668814.21755.6706-0.531323.40880.0014-0.5441-0.3410.051-0.04390.61550.1575-0.8380.0425-0.0555-0.04320.0351-0.02470.045-0.015116.3003-15.52211.362
112.62163.7465-2.77445.3793-4.15394.35250.1237-0.17580.1930.5683-0.05430.3525-0.48760.0506-0.06940.0048-0.0252-0.01460.04150.0095-0.026924.6405-8.739317.9928
125.84080.6695-8.4257.6424-3.97722.5093-0.1714-0.00370.4492-0.1968-0.0509-0.9442-0.7230.4840.22240.0077-0.1625-0.0606-0.01640.05380.035234.2135-2.54554.5235
1321.112-7.526-2.193124.25769.86916.0006-0.02980.7299-0.7215-0.6773-0.59741.7919-0.8572-1.29450.62720.0430.0704-0.05350.0647-0.0687-0.000813.763-11.8266-10.0007
142.399-0.25571.84172.3704-0.5334.4850.0308-0.0501-0.06990.0252-0.1137-0.3059-0.02710.41790.083-0.1005-0.01210.03340.00220.0194-0.022831.8338-15.73362.0172
154.68420.14794.91932.995-0.866113.53170.1151-0.1171-0.225-0.3115-0.1518-0.1540.3203-0.10560.0368-0.05990.01180.051-0.0698-0.0254-0.022524.7489-22.1103-7.2875
168.128-9.2487-4.092325.036311.50127.7957-0.17750.219-0.0391-0.28060.3315-0.2201-0.25690.0822-0.154-0.0121-0.04520.0362-0.03310.0548-0.060525.8963-4.6437-6.4096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 368 - 43
2X-RAY DIFFRACTION2AA37 - 4244 - 49
3X-RAY DIFFRACTION3AA43 - 6350 - 70
4X-RAY DIFFRACTION4AA64 - 7271 - 79
5X-RAY DIFFRACTION5BB2 - 199 - 26
6X-RAY DIFFRACTION6BB20 - 3027 - 37
7X-RAY DIFFRACTION7BB31 - 5338 - 60
8X-RAY DIFFRACTION8BB54 - 7261 - 79
9X-RAY DIFFRACTION9CC0 - 367 - 43
10X-RAY DIFFRACTION10CC37 - 4444 - 51
11X-RAY DIFFRACTION11CC45 - 5952 - 66
12X-RAY DIFFRACTION12CC60 - 7167 - 78
13X-RAY DIFFRACTION13DD1 - 78 - 14
14X-RAY DIFFRACTION14DD8 - 3715 - 44
15X-RAY DIFFRACTION15DD38 - 5245 - 59
16X-RAY DIFFRACTION16DD53 - 7260 - 79

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