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- PDB-6n34: Crystal structure of the BTB domain of Human NS1-BP -

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Basic information

Entry
Database: PDB / ID: 6n34
TitleCrystal structure of the BTB domain of Human NS1-BP
ComponentsInfluenza virus NS1A-binding protein
KeywordsSPLICING / mRNA export
Function / homology
Function and homology information


transcription by RNA polymerase III / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of protein ubiquitination / intrinsic apoptotic signaling pathway / RNA splicing / spliceosomal complex / response to virus / mRNA processing / transcription regulator complex / cytoskeleton ...transcription by RNA polymerase III / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of protein ubiquitination / intrinsic apoptotic signaling pathway / RNA splicing / spliceosomal complex / response to virus / mRNA processing / transcription regulator complex / cytoskeleton / nucleoplasm / cytosol
Similarity search - Function
BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. ...BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Influenza virus NS1A-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, K. / Shang, G. / Padavannil, A. / Fontoura, B. / Chook, Y.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch Foundation1-1532 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural-functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression.
Authors: Zhang, K. / Shang, G. / Padavannil, A. / Wang, J. / Sakthivel, R. / Chen, X. / Kim, M. / Thompson, M.G. / Garcia-Sastre, A. / Lynch, K.W. / Chen, Z.J. / Chook, Y.M. / Fontoura, B.M.A.
History
DepositionNov 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Influenza virus NS1A-binding protein
B: Influenza virus NS1A-binding protein


Theoretical massNumber of molelcules
Total (without water)33,1682
Polymers33,1682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-37 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.866, 72.599, 92.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Influenza virus NS1A-binding protein / NS1-binding protein / Aryl hydrocarbon receptor-associated protein 3 / Kelch-like protein 39


Mass: 16583.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: IVNS1ABP, ARA3, FLARA3, KIAA0850, KLHL39, NS1, NS1BP, HSPC068
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y6Y0

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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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 7423 / % possible obs: 98.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.057 / Rrim(I) all: 0.139 / Χ2: 1.404 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.70.7433330.5530.4960.8990.73396.2
2.85-2.93.10.5913580.6630.3740.7040.86696.8
2.9-2.963.50.5273480.7740.310.6160.7897.5
2.96-3.023.90.5913760.7050.3310.6820.72897.2
3.02-3.084.30.8093400.7020.4260.9190.83598
3.08-3.154.70.793640.7560.3950.8870.85798.1
3.15-3.235.30.5833730.8420.2810.6490.84798.9
3.23-3.325.60.5933530.870.2760.6570.86597.8
3.32-3.426.10.5223530.9040.2320.5731.00999.4
3.42-3.536.10.3653840.9310.1630.4011.31699.2
3.53-3.655.90.583640.9130.2610.6371.968100
3.65-3.86.10.2793740.950.1240.3062.9100
3.8-3.976.40.1893680.9780.0810.2061.54100
3.97-4.186.60.1253830.9910.0530.1361.431100
4.18-4.446.50.0993720.9930.0420.1081.63100
4.44-4.796.50.0833770.9960.0350.091.406100
4.79-5.276.30.0863910.9920.0370.0931.559100
5.27-6.036.30.0913920.9930.0390.11.637100
6.03-7.5960.0893810.9950.040.0981.637100
7.59-505.40.0994390.9970.0440.1091.48298.9

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
PHENIXmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I3N

3i3n


Resolution: 2.8→38.166 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2974 730 10.01 %
Rwork0.2249 6564 -
obs0.2321 7294 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.57 Å2 / Biso mean: 98.1473 Å2 / Biso min: 62.89 Å2
Refinement stepCycle: final / Resolution: 2.8→38.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 0 0 1884
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091914
X-RAY DIFFRACTIONf_angle_d0.9922573
X-RAY DIFFRACTIONf_chiral_restr0.049289
X-RAY DIFFRACTIONf_plane_restr0.004328
X-RAY DIFFRACTIONf_dihedral_angle_d13.791165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-3.01620.38841380.29281244138297
3.0162-3.31960.37731420.27691275141798
3.3196-3.79960.38821470.27151319146699
3.7996-4.78560.26741470.201513191466100
4.7856-38.16970.26041560.206914071563100
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)
11.7366-0.25121.51873.0278-2.76667.1138-0.28780.2366-0.41850.40760.0683-0.0489-0.4851-0.03090.07040.78120.00750.08760.6633-0.02030.918328.276351.313216.5788
23.3601-2.6484.2783.1819-3.53596.047-0.2268-0.442-0.11290.45680.3269-0.1457-0.6318-0.33440.0420.81620.15080.18650.7059-0.02170.939937.175642.903836.2154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 6:129)A6 - 129
2X-RAY DIFFRACTION2(chain B and resseq 4:128)B4 - 128

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