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- PDB-6q8f: Nterminal domain of human SMU1 -

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Basic information

Entry
Database: PDB / ID: 6q8f
TitleNterminal domain of human SMU1
ComponentsWD40 repeat-containing protein SMU1
KeywordsSPLICING / Splicing factor
Function / homology
Function and homology information


U2-type precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / precatalytic 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-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
WD40 repeat-containing protein SMU1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: WD40 repeat-containing protein SMU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5924
Polymers115,3482
Non-polymers2452
Water3,909217
1
B: WD40 repeat-containing protein SMU1
hetero molecules

A: WD40 repeat-containing protein SMU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5924
Polymers115,3482
Non-polymers2452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4880 Å2
ΔGint-40 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.183, 41.225, 123.599
Angle α, β, γ (deg.)90.00, 91.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 57673.797 Da / Num. of mol.: 2
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-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 16-20 % PEG 10K, 0.1 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 31423 / % possible obs: 97.2 % / Redundancy: 5.6 % / Rrim(I) all: 0.064 / Net I/σ(I): 22.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.36 / Num. unique obs: 1956 / Rrim(I) all: 0.536 / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XSCALEdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→39.14 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.483 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21375 1610 5.1 %RANDOM
Rwork0.17442 ---
obs0.17644 29818 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.692 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å2-0 Å21.19 Å2
2---0.55 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.9→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 15 217 3256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133089
X-RAY DIFFRACTIONr_bond_other_d00.0173001
X-RAY DIFFRACTIONr_angle_refined_deg1.491.644183
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5716964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00622.284162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02515573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6351524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023359
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02593
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_it3.5142.5081521
X-RAY DIFFRACTIONr_mcbond_other3.5142.5051519
X-RAY DIFFRACTIONr_mcangle_it5.0593.7341893
X-RAY DIFFRACTIONr_mcangle_other5.0583.7341893
X-RAY DIFFRACTIONr_scbond_it4.2552.8941568
X-RAY DIFFRACTIONr_scbond_other4.2542.8941569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4164.22290
X-RAY DIFFRACTIONr_long_range_B_refined9.08129.8873545
X-RAY DIFFRACTIONr_long_range_B_other9.09929.8363508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 108 -
Rwork0.258 1826 -
obs--81.36 %

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