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- PDB-6zlc: Non-specific dsRNA recognition by wildtype H7N1 RNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 6zlc
TitleNon-specific dsRNA recognition by wildtype H7N1 RNA-binding domain
Components
  • Non-structural protein 1
  • RNA (5'-R(*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*U)-3')
KeywordsVIRAL PROTEIN / INFLUENZA A VIRUS / RNA BINDING DOMAIN / RNA-PROTEIN COMPLEX
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 / protein serine/threonine kinase inhibitor activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding
Similarity search - Domain/homology
NITRATE ION / RNA / RNA (> 10) / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCoste, F. / Wacquiez, A. / Marc, D. / Castaing, B.
CitationJournal: Viruses / Year: 2020
Title: Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1.
Authors: Wacquiez, A. / Coste, F. / Kut, E. / Gaudon, V. / Trapp, S. / Castaing, B. / Marc, D.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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: Non-structural protein 1
B: Non-structural protein 1
C: RNA (5'-R(*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*U)-3')
D: RNA (5'-R(*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,15410
Polymers29,7144
Non-polymers4406
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-62 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.596, 103.596, 102.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Non-structural protein 1 / NS1


Mass: 8817.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/turkey/Italy/977/1999(H7N1))
Strain: A/turkey/Italy/977/1999(H7N1) / Gene: ns1, NS, NS1 / Variant: A/turkey/Italy/977/1999(H7N1) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PST0
#2: RNA chain RNA (5'-R(*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*U)-3')


Mass: 6039.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.61 Å3/Da / Density % sol: 73.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200mM ammonium nitrate, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→46.33 Å / Num. obs: 25358 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 62.02 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.8
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2431 / CC1/2: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZKO

2zko


Resolution: 2.3→46.33 Å / SU ML: 0.3394 / Cross valid method: FREE R-VALUE / Phase error: 22.7724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 1233 4.87 %
Rwork0.191 24069 -
obs0.1923 25302 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 798 26 56 2045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422088
X-RAY DIFFRACTIONf_angle_d0.66682986
X-RAY DIFFRACTIONf_chiral_restr0.0319368
X-RAY DIFFRACTIONf_plane_restr0.0036245
X-RAY DIFFRACTIONf_dihedral_angle_d4.69251177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.33771470.3122602X-RAY DIFFRACTION99.93
2.39-2.50.34091560.29312592X-RAY DIFFRACTION99.96
2.5-2.630.32691630.27422611X-RAY DIFFRACTION100
2.63-2.80.30371480.26412628X-RAY DIFFRACTION100
2.8-3.010.27411090.26522669X-RAY DIFFRACTION100
3.01-3.320.28891140.22812682X-RAY DIFFRACTION100
3.32-3.80.19971350.17612683X-RAY DIFFRACTION100
3.8-4.780.17551360.14072715X-RAY DIFFRACTION100
4.78-46.330.171250.1662887X-RAY DIFFRACTION99.77
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)
18.68204049493-5.606253175515.200388095514.07682051937-4.948634289748.505832831311.135398636491.92899850350.520727375759-0.889736303223-2.59575463549-0.131286024123-0.6229340646672.114740551811.005469065820.9553566964740.0865255257039-0.07648788184391.3728006250.01434005850670.91100993371635.930736982311.1894648568-1.47726253921
22.423079500130.16704492082-0.02326796941496.12485243648-3.374661906551.99987346320.03207575599240.2116809142-0.0599944638974-0.532487960983-0.166626206691-0.05360472691490.1776877934780.007692405824010.1263691438950.5831694793620.01885204337840.01748650857290.574092183648-0.04945501387140.38838279699841.3387263392-9.25852070359-2.76324336802
35.03384301052-5.23140357093-4.966940672145.470032424275.227934391975.051093270310.4933702922341.4075127727-1.03251800202-0.424755190014-0.428536111611-0.1119405364410.590436114754-0.6002830548820.05412663589381.097458254680.03064718388080.04739478597380.859671808593-0.140352840290.74506015453941.2689057314-26.2064568915-4.06978321724
41.40455233759-0.3998458841570.7139295371763.43148456198-3.669765251744.306968559220.003196447750390.260485851111-0.15559633011-0.183734970720.3935060145630.899717913090.239986745509-0.234365043273-0.3537115197390.574034385004-0.01470590647560.01637981318610.568353290919-0.07675393161620.50593260200732.4419847681-11.6633963516-1.11798095223
53.6921628144-2.87188458752-1.443690572219.86093962814-2.405542829728.87923521061-0.3481025121180.626912678427-0.156951923996-0.0352203297923-0.24923662889-0.722002604053-0.4710819758171.050568135080.5444317770980.546756550598-0.02649858519030.04652989652970.4545483183960.012448368320.42740726922447.5213902694-4.42865503323-4.6128986254
61.843985001840.596196906091.32311585215.690044235461.270241713573.971783467180.113583414012-0.0117077864954-0.352311720155-0.492585230702-0.44808192648-0.1801759040440.09923720839660.07360383491990.3002456978820.6018114139960.01193441602170.09504744056960.5821455745170.006485840230.53371755904846.1479340428-17.75597264796.31651512094
71.45559220427-1.0245846311-0.1243045038487.82378438038-2.245104561652.94011334080.0177132398883-0.113547357484-0.06094270684230.469737990988-0.2437965133210.0902743630171-0.3212345293890.1749634619410.2470322933990.601876436881-0.08039155207460.01752826138250.585614863488-0.0473333043720.43195799646241.4894479856-11.16732114511.9892677626
87.26812006318-0.5457457104714.141781737527.56879294532-3.523616688956.297752389050.1009510565780.515553321954-0.552429651623-0.668328993288-0.206671137556-0.5541839729230.6004636472571.53181435570.1421488851050.5956464064060.1140519137340.110685696090.483635528425-0.02013354327410.59691199499251.889432201-21.15515196712.28546496985
94.168724682214.71198925051-2.219255939737.919015860780.5879270870116.19549876783-0.440211882259-0.720673725321-1.218511854910.432748248061-0.0001676581343881.701451183941.129619341520.2281541436380.5276066595440.8475312810750.005057977895760.1421672813550.5448679936850.08514106736661.0731741813631.8623989062-29.527533898717.8407288663
102.284916721170.948530566744-0.3831364417196.2778712342-1.51431781266.75315367535-0.1544429360570.139733855550.527904845630.373785467636-0.06686403743131.005009949070.141045076854-0.3514558299730.1602113959580.679355719918-0.07037247008460.04395030638630.649308227612-0.09835740353690.85073283199323.8829672139-16.83622016487.75442260484
114.01815953694-0.877945049515-0.59016824193.88815881418-3.296782760734.902817928210.164890904133-0.226368711615-0.3349133162450.372926209883-0.1006187460431.16887064344-0.419283184411-0.261873906279-0.159031462410.7180206650890.07037809218460.1102833862650.607000128856-0.1175831530480.82650644600126.45955881271.3893652120111.5160561353
124.9010793656-2.971371696470.2833118655623.92341537618-1.632958369085.694234737070.02563427614840.0281518591330.00181796810560.559937539087-0.08663383468390.826480753666-0.2404901049380.170911227828-0.1130699779290.622170314992-0.1002118626130.07595986548540.488500076869-0.0286952671760.71697795216725.5969154699-3.368217578239.83303173178
134.64534211882-1.12123485863-1.512244655253.04432197282-1.970396655933.543107782740.380406932148-0.13630101174-0.4469164974940.389265145205-0.2554214423460.5171383612520.214226396897-0.16679371403-0.1383152657650.938601156155-0.1954133602020.07917784418990.625795472976-6.58582189361E-60.91097722863327.010029455-28.083924471411.0217203484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 2 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 29 )
4X-RAY DIFFRACTION4chain 'A' and (resid 30 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 73 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 50 )
8X-RAY DIFFRACTION8chain 'B' and (resid 51 through 72 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 5 )
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 10 )
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 19 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 10 )
13X-RAY DIFFRACTION13chain 'D' and (resid 11 through 19 )

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