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- PDB-6q8j: Nterminal domain of human SMU1 in complex with LSP641 -

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Basic information

Entry
Database: PDB / ID: 6q8j
TitleNterminal domain of human SMU1 in complex with LSP641
ComponentsWD40 repeat-containing protein SMU1
KeywordsSPLICING / Splicing factor / influenza virus
Function / homology
Function and homology information


U2-type precatalytic spliceosome / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / nuclear speck / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
WD40 repeat-containing protein SMU1 / LisH-like dimerisation domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...WD40 repeat-containing protein SMU1 / LisH-like dimerisation domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-XS4 / WD40 repeat-containing protein SMU1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTengo, L. / Le Corre, L. / Fournier, G. / Ashraf, U. / Busca, P. / Rameix-Welti, M.-A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.-O. ...Tengo, L. / Le Corre, L. / Fournier, G. / Ashraf, U. / Busca, P. / Rameix-Welti, M.-A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.-O. / Pietrancosta, N. / Naffakh, N. / McCarthy, A.A. / Crepin, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Destabilization of the human RED-SMU1 splicing complex as a basis for host-directed antiinfluenza strategy.
Authors: Ashraf, U. / Tengo, L. / Le Corre, L. / Fournier, G. / Busca, P. / McCarthy, A.A. / Rameix-Welti, M.A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.O. / Pietrancosta, ...Authors: Ashraf, U. / Tengo, L. / Le Corre, L. / Fournier, G. / Busca, P. / McCarthy, A.A. / Rameix-Welti, M.A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.O. / Pietrancosta, N. / Crepin, T. / Naffakh, N.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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: WD40 repeat-containing protein SMU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4173
Polymers22,1151
Non-polymers1,3022
Water1,838102
1
A: WD40 repeat-containing protein SMU1
hetero molecules

A: WD40 repeat-containing protein SMU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8346
Polymers44,2312
Non-polymers2,6034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3900 Å2
ΔGint-30 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.193, 72.193, 183.164
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein WD40 repeat-containing protein SMU1 / Smu-1 suppressor of mec-8 and unc-52 protein homolog


Mass: 22115.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMU1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TAY7
#2: Chemical ChemComp-XS4 / 1-~{tert}-butyl-3-[6-(3,5-dimethoxyphenyl)-2-[[1-[1-(phenylmethyl)piperidin-4-yl]-1,2,3-triazol-4-yl]methylamino]pyrido[2,3-d]pyrimidin-7-yl]urea


Mass: 650.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H42N10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bis-Tris pH 6, 16-20 % PEG 10K, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→44 Å / Num. obs: 26383 / % possible obs: 97.4 % / Redundancy: 5.27 % / Rrim(I) all: 0.051 / Net I/σ(I): 16.86
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 5.32 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3140 / Rrim(I) all: 0.762 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q8F

6q8f


Resolution: 1.8→43.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.684 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22007 1343 5.1 %RANDOM
Rwork0.16061 ---
obs0.16359 25046 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.09 Å2-0 Å2
2---0.19 Å20 Å2
3---0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.8→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 96 102 1687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131646
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171571
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.732243
X-RAY DIFFRACTIONr_angle_other_deg1.391.6433636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57621.92883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.021513
X-RAY DIFFRACTIONr_chiral_restr0.0680.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.021785
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02330
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.2964.168759
X-RAY DIFFRACTIONr_mcbond_other7.2614.164758
X-RAY DIFFRACTIONr_mcangle_it7.9526.254949
X-RAY DIFFRACTIONr_mcangle_other7.9626.256950
X-RAY DIFFRACTIONr_scbond_it10.6765.029887
X-RAY DIFFRACTIONr_scbond_other10.6815.04888
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.8917.311290
X-RAY DIFFRACTIONr_long_range_B_refined10.28249.1912038
X-RAY DIFFRACTIONr_long_range_B_other10.30649.0192019
X-RAY DIFFRACTIONr_rigid_bond_restr6.24633216
X-RAY DIFFRACTIONr_sphericity_free26.291565
X-RAY DIFFRACTIONr_sphericity_bonded29.91653215
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 101 -
Rwork0.219 1805 -
obs--97.49 %

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