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- PDB-1xeq: Crystal tructure of RNA binding domain of influenza B virus non-s... -

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Basic information

Entry
Database: PDB / ID: 1xeq
TitleCrystal tructure of RNA binding domain of influenza B virus non-structural protein
ComponentsNonstructural protein NS1
KeywordsVIRAL PROTEIN / Influenza B virus / RNA binding domain / non-structural protein / NS1B / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host ISG15-protein conjugation / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / RNA binding
Similarity search - Function
Influenza B 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
BROMIDE ION / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKhan, J.A. / Yin, C. / Krug, R.M. / Montelione, G.T. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Conserved surface features form the double-stranded RNA binding site of non-structural protein 1 (NS1) from influenza A and B viruses.
Authors: Yin, C. / Khan, J.A. / Swapna, G.V. / Ertekin, A. / Krug, R.M. / Tong, L. / Montelione, G.T.
History
DepositionSep 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Feb 14, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

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Assembly

Deposited unit
A: Nonstructural protein NS1
B: Nonstructural protein NS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28121
Polymers23,7632
Non-polymers1,51819
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-26 kcal/mol
Surface area10470 Å2
MethodPISA
2
A: Nonstructural protein NS1
B: Nonstructural protein NS1
hetero molecules

A: Nonstructural protein NS1
B: Nonstructural protein NS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,56342
Polymers47,5274
Non-polymers3,03638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+2/31
Buried area13090 Å2
ΔGint-74 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.032, 102.032, 108.843
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 4 / Auth seq-ID: 20 - 85 / Label seq-ID: 20 - 85

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Nonstructural protein NS1


Mass: 11881.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (B/Lee/40) / Genus: Influenzavirus BInfluenza B virus / Species: Influenza B virus / Strain: B/Lee/40 / Gene: 8 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03502
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 3.9
Details: pH 3.9, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9197 Å
DetectorDate: Sep 29, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.1→29.6 Å / Num. all: 18879 / Num. obs: 18879 / Biso Wilson estimate: 22.89 Å2
Reflection shellResolution: 2.1→2.12 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.6 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.891 / SU B: 3.298 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25567 1018 5.1 %RANDOM
Rwork0.21335 ---
all0.21548 18879 --
obs0.21548 18879 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.898 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 19 234 1676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0211451
X-RAY DIFFRACTIONr_bond_other_d0.0030.021340
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.9691938
X-RAY DIFFRACTIONr_angle_other_deg1.07233128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355172
X-RAY DIFFRACTIONr_chiral_restr0.1380.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021585
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02301
X-RAY DIFFRACTIONr_nbd_refined0.2720.2459
X-RAY DIFFRACTIONr_nbd_other0.2560.21670
X-RAY DIFFRACTIONr_nbtor_other0.1010.2871
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3310.2179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.430.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4660.229
X-RAY DIFFRACTIONr_mcbond_it1.3611.5867
X-RAY DIFFRACTIONr_mcangle_it2.26821389
X-RAY DIFFRACTIONr_scbond_it3.6433584
X-RAY DIFFRACTIONr_scangle_it5.5124.5549
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1083 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.730.5
medium thermal2.892
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 65
Rwork0.211 1366
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)
10.2266-0.2023-0.08250.3089-0.04950.12190.0404-0.0644-0.09440.077-0.00350.01060.0869-0.0462-0.03690.0955-0.0425-0.02960.04950.00740.071168.641121.586241.2112
20.55220.0619-0.02380.04190.05850.32590.01090.0153-0.08350.03630.02430.03030.05660.0168-0.03510.0765-0.0152-0.03460.0435-0.03410.057276.456425.629327.3435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 10315 - 103
2X-RAY DIFFRACTION2BB9 - 899 - 89

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