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- PDB-5yy8: Crystal structure of the Kelch domain of human NS1-BP -

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Basic information

Entry
Database: PDB / ID: 5yy8
TitleCrystal structure of the Kelch domain of human NS1-BP
ComponentsInfluenza virus NS1A-binding protein
KeywordsPROTEIN BINDING / Host-virus interaction
Function / homology
Function and homology information


Cul3-RING ubiquitin ligase complex / negative regulation of intrinsic apoptotic signaling pathway / transcription by RNA polymerase III / ubiquitin-like ligase-substrate adaptor activity / negative regulation of protein ubiquitination / intrinsic apoptotic signaling pathway / RNA splicing / spliceosomal complex / response to virus / mRNA processing ...Cul3-RING ubiquitin ligase complex / negative regulation of intrinsic apoptotic signaling pathway / transcription by RNA polymerase III / ubiquitin-like ligase-substrate adaptor activity / negative regulation of protein ubiquitination / intrinsic apoptotic signaling pathway / RNA splicing / spliceosomal complex / response to virus / mRNA processing / transcription regulator complex / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Kelch-type beta propeller / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller ...Kelch-type beta propeller / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 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 / SAD / Resolution: 1.979 Å
AuthorsGuo, L. / Liu, Y. / Liang, H.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of the Kelch domain of human NS1-binding protein at 1.98 angstrom resolution.
Authors: Guo, L. / Liu, Y.
History
DepositionDec 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)37,0301
Polymers37,0301
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11880 Å2
Unit cell
Length a, b, c (Å)61.556, 61.556, 140.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 37030.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IVNS1ABP, ARA3, FLARA3, KIAA0850, NS1, NS1BP, HSPC068 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6Y0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Ammonium citrate tribasic pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.979→50 Å / Num. obs: 41146 / % possible obs: 98.93 % / Redundancy: 20.9 % / Biso Wilson estimate: 33.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08406 / Rpim(I) all: 0.0191 / Rrim(I) all: 0.08628 / Net I/σ(I): 20.64
Reflection shellResolution: 1.979→2.05 Å / Rmerge(I) obs: 0.4192 / Mean I/σ(I) obs: 7.74 / Num. unique obs: 2037 / CC1/2: 0.974 / Rpim(I) all: 0.09841 / Rrim(I) all: 0.4311 / % possible all: 93.58

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.979→28.193 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 3743 9.1 %
Rwork0.1886 --
obs0.1924 41146 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.979→28.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 0 134 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062231
X-RAY DIFFRACTIONf_angle_d0.7753029
X-RAY DIFFRACTIONf_dihedral_angle_d10.3521310
X-RAY DIFFRACTIONf_chiral_restr0.051321
X-RAY DIFFRACTIONf_plane_restr0.004399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.979-2.00410.33951220.24841212X-RAY DIFFRACTION88
2.0041-2.03040.28211340.22941302X-RAY DIFFRACTION95
2.0304-2.05820.25921420.22021421X-RAY DIFFRACTION100
2.0582-2.08760.26141340.21761391X-RAY DIFFRACTION100
2.0876-2.11880.21091480.20731414X-RAY DIFFRACTION100
2.1188-2.15190.24691420.20641356X-RAY DIFFRACTION100
2.1519-2.18720.23181360.2061403X-RAY DIFFRACTION100
2.1872-2.22490.31531460.20711397X-RAY DIFFRACTION100
2.2249-2.26530.24261400.2041404X-RAY DIFFRACTION100
2.2653-2.30880.24871380.20291343X-RAY DIFFRACTION100
2.3088-2.3560.23951440.19351441X-RAY DIFFRACTION100
2.356-2.40720.24871270.20081360X-RAY DIFFRACTION100
2.4072-2.46310.2511400.21441472X-RAY DIFFRACTION100
2.4631-2.52470.2841380.2061353X-RAY DIFFRACTION100
2.5247-2.59290.30311480.20891405X-RAY DIFFRACTION100
2.5929-2.66910.25251400.20321425X-RAY DIFFRACTION100
2.6691-2.75520.29351420.20461356X-RAY DIFFRACTION100
2.7552-2.85360.24041360.19071393X-RAY DIFFRACTION100
2.8536-2.96770.241480.19691403X-RAY DIFFRACTION100
2.9677-3.10260.23331400.19761391X-RAY DIFFRACTION100
3.1026-3.2660.25811420.19811412X-RAY DIFFRACTION100
3.266-3.47030.23341200.19321411X-RAY DIFFRACTION100
3.4703-3.73770.21931480.18281372X-RAY DIFFRACTION100
3.7377-4.11280.2261370.16711436X-RAY DIFFRACTION100
4.1128-4.70550.14611300.13991366X-RAY DIFFRACTION99
4.7055-5.91940.2061440.16381397X-RAY DIFFRACTION100
5.9194-28.19620.2241370.211367X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 24.7083 Å / Origin y: -17.3827 Å / Origin z: -14.4538 Å
111213212223313233
T0.1895 Å2-0.0536 Å20.0356 Å2-0.1477 Å2-0.0352 Å2--0.1688 Å2
L0.5374 °2-0.0626 °2-0.0148 °2-0.4748 °2-0.0822 °2--0.5967 °2
S0.0332 Å °0.0448 Å °-0.0382 Å °0.0165 Å °0.0115 Å °0.0179 Å °-0.0014 Å °0.0707 Å °0 Å °
Refinement TLS groupSelection details: all

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