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- PDB-6n3h: Crystal structure of Kelch domain of the human NS1 binding protein -

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Basic information

Entry
Database: PDB / ID: 6n3h
TitleCrystal structure of Kelch domain of the human NS1 binding protein
ComponentsInfluenza virus NS1A-binding protein
KeywordsSPLICING / mRNA export / mRNA splicing
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 / transcription regulator complex / cytoskeleton / nucleoplasm / cytosol
Similarity search - Function
Kelch-type beta propeller / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain ...Kelch-type beta propeller / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Influenza virus NS1A-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, K. / Shang, G. / Padavannil, A. / Fontoura, B.M.A. / Chook, Y.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationI-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 15, 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
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

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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)73,4672
Polymers73,4672
Non-polymers00
Water2,144119
1
A: Influenza virus NS1A-binding protein


Theoretical massNumber of molelcules
Total (without water)36,7331
Polymers36,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Influenza virus NS1A-binding protein


Theoretical massNumber of molelcules
Total (without water)36,7331
Polymers36,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.196, 61.885, 87.339
Angle α, β, γ (deg.)90.000, 95.180, 90.000
Int Tables number4
Space group name H-MP1211

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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: 36733.320 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 3.0 M NaCl

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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: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 25558 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.085 / Rrim(I) all: 0.218 / Χ2: 0.905 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.6-2.645.912440.680.4670.51399.4
2.64-2.696.112610.8160.3810.52799.90.8630.945
2.69-2.745.812780.8750.2570.5251000.5610.619
2.74-2.85.912540.9110.1920.53399.80.4240.466
2.8-2.866.512760.9440.2110.5461000.4940.538
2.86-2.93712680.9430.2160.5811000.530.572
2.93-37.212630.9640.1740.5941000.4350.469
3-3.087.312920.9720.1660.6111000.4190.451
3.08-3.177.312510.9760.140.6171000.3540.38
3.17-3.287.312710.9860.1180.7051000.2990.322
3.28-3.397.312860.9870.10.7111000.2540.273
3.39-3.537.312730.9910.0880.7721000.2220.239
3.53-3.696.712930.9630.162.13799.90.3760.41
3.69-3.887.112580.9780.1271.711000.3140.339
3.88-4.137.313010.9930.0741.3781000.1870.202
4.13-4.457.212710.9950.0421.181000.1060.114
4.45-4.897.212920.9950.0371.291000.0930.101
4.89-5.67.112820.9960.0371.1011000.0930.1
5.6-7.05713020.9950.0370.8081000.0910.098
7.05-506.913420.9980.0220.97499.80.0540.059

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-30001.8.4_1496data collection
HKL-2000data scaling
HKL-30003.24data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XN4

2xn4


Resolution: 2.6→43.491 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71
RfactorNum. reflection% reflection
Rfree0.2345 1218 5 %
Rwork0.2106 --
obs0.2118 24337 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.81 Å2 / Biso mean: 42.6235 Å2 / Biso min: 18.86 Å2
Refinement stepCycle: final / Resolution: 2.6→43.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 0 120 4592
Biso mean---40.5 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034583
X-RAY DIFFRACTIONf_angle_d0.7766223
X-RAY DIFFRACTIONf_chiral_restr0.031656
X-RAY DIFFRACTIONf_plane_restr0.003818
X-RAY DIFFRACTIONf_dihedral_angle_d13.3251645
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.70410.31511030.27631955205873
2.7041-2.82710.30651240.28212362248689
2.8271-2.97620.29791400.2662644278499
2.9762-3.16260.27351380.257726452783100
3.1626-3.40670.26831430.241327032846100
3.4067-3.74930.25661370.2442619275698
3.7493-4.29150.22891430.175727182861100
4.2915-5.40520.1741430.147727012844100
5.4052-43.49690.19151470.19427722919100
Refinement TLS params.Method: refined / Origin x: 157.8843 Å / Origin y: 76.9737 Å / Origin z: 114.326 Å
111213212223313233
T0.24 Å2-0.0401 Å20.0151 Å2-0.2682 Å2-0.0405 Å2--0.2009 Å2
L0.2613 °2-0.3526 °20.1794 °2-0.9666 °2-0.3699 °2--0.3693 °2
S-0.0012 Å °0.0532 Å °-0.0207 Å °-0.1199 Å °0.0206 Å °-0.0871 Å °-0.0346 Å °0.0512 Å °-0.0301 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA347 - 650
2X-RAY DIFFRACTION1allB349 - 637
3X-RAY DIFFRACTION1allS1 - 133

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