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- PDB-1ail: N-TERMINAL FRAGMENT OF NS1 PROTEIN FROM INFLUENZA A VIRUS -

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Basic information

Entry
Database: PDB / ID: 1ail
TitleN-TERMINAL FRAGMENT OF NS1 PROTEIN FROM INFLUENZA A VIRUS
ComponentsNONSTRUCTURAL PROTEIN NS1
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / NONSTRUCTURAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell nucleus / identical protein 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 / 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 / MIRAS / Resolution: 1.9 Å
AuthorsLiu, J. / Lynch, P.A. / Chien, C. / Montelione, G.T. / Krug, R.M. / Berman, H.M.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein.
Authors: Liu, J. / Lynch, P.A. / Chien, C.Y. / Montelione, G.T. / Krug, R.M. / Berman, H.M.
History
DepositionApr 21, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NONSTRUCTURAL PROTEIN NS1


Theoretical massNumber of molelcules
Total (without water)8,3381
Polymers8,3381
Non-polymers00
Water61334
1
A: NONSTRUCTURAL PROTEIN NS1

A: NONSTRUCTURAL PROTEIN NS1


Theoretical massNumber of molelcules
Total (without water)16,6772
Polymers16,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2040 Å2
ΔGint-16 kcal/mol
Surface area8120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)38.651, 38.651, 82.928
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 NONSTRUCTURAL PROTEIN NS1


Mass: 8338.430 Da / Num. of mol.: 1 / Fragment: RNA-BINDING DOMAIN / Source method: isolated from a natural source
Source: (natural) Influenza A virus (A/Udorn/307/1972(H3N2))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: A/Udorn/307/72 H3N2 / References: UniProt: P03495
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 4

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 34 %
Crystal growpH: 6.5
Details: NATIVE CRYSTALS WERE GROWN FROM 50MM NAH2PO4, 100MM NACL, 1MM NAN3 AT PH 6.5; MERCURY DERIVATIVE CRYSTAL WAS PREPARED BY SOAKING THE NATIVE CRYSTAL IN 2MM CH3HGCL WITH 10% PEG 6000 AT PH 8.0; ...Details: NATIVE CRYSTALS WERE GROWN FROM 50MM NAH2PO4, 100MM NACL, 1MM NAN3 AT PH 6.5; MERCURY DERIVATIVE CRYSTAL WAS PREPARED BY SOAKING THE NATIVE CRYSTAL IN 2MM CH3HGCL WITH 10% PEG 6000 AT PH 8.0; PLATINUM DERIVATIVE CRYSTAL WAS PREPARED BY SOAKING THE NATIVE CRYSTAL IN 4MM PT(NH3)2CL2 WITH 10% PEG 6000 AT PH 6.5.
PH range: 6.5 for native,8.0 for Mg derivative,6.5 for Pt derative
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium phosphate1drop
2100 mM1dropNaCl
31 mM1dropNaN3
420.8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 5318 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.065 / Net I/σ(I): 18
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.217 / % possible all: 90.7
Reflection
*PLUS
Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
PHASESphasing
SOLOMONphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→20 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.229 494 10 %RANDOM
Rwork0.182 ---
obs-5104 95 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms558 0 0 34 592
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_deg1.3

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