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- PDB-5en6: Crystal structure of the Smu1-RED complex (SeMet) of Caenorhabdit... -

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Basic information

Entry
Database: PDB / ID: 5en6
TitleCrystal structure of the Smu1-RED complex (SeMet) of Caenorhabditis elegans
Components
  • SMU-1
  • Suppressor of Mec and Unc defects
KeywordsSPLICING / LisH motif / CTLH / dimer / heterotetramer / splicing factor
Function / homology
Function and homology information


nematode larval development / muscle organ morphogenesis / mechanosensory behavior / locomotion / U2-type precatalytic spliceosome / embryo development ending in birth or egg hatching / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / neuron development / RNA splicing ...nematode larval development / muscle organ morphogenesis / mechanosensory behavior / locomotion / U2-type precatalytic spliceosome / embryo development ending in birth or egg hatching / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / neuron development / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / nucleolus / protein homodimerization activity / identical protein binding / nucleus
Similarity search - Function
Protein RED, C-terminal / RED-like, N-terminal / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / 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. ...Protein RED, C-terminal / RED-like, N-terminal / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / 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 / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Smu-1 suppressor of mec-8 and unc-52 protein / Smu-2 suppressor of mec-8 and unc-52 protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 3.103 Å
AuthorsUlrich, A.K.C. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
DFGWA1126/7-1 Germany
CitationJournal: to be published
Title: Crystal structure of the Smu1-RED complex (SeMet) of Caenorhabditis elegans
Authors: Ulrich, A.K.C. / Schulz, J.F. / Kamprad, A. / Schuetze, T. / Wahl, M.C.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMU-1
B: SMU-1
C: Suppressor of Mec and Unc defects
D: Suppressor of Mec and Unc defects


Theoretical massNumber of molelcules
Total (without water)55,6284
Polymers55,6284
Non-polymers00
Water1,00956
1
A: SMU-1
D: Suppressor of Mec and Unc defects

A: SMU-1
D: Suppressor of Mec and Unc defects


Theoretical massNumber of molelcules
Total (without water)55,6284
Polymers55,6284
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area4930 Å2
ΔGint-47 kcal/mol
Surface area22580 Å2
MethodPISA
2
B: SMU-1
C: Suppressor of Mec and Unc defects

B: SMU-1
C: Suppressor of Mec and Unc defects


Theoretical massNumber of molelcules
Total (without water)55,6284
Polymers55,6284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_353-x-2,y,-z-3/21
Buried area5020 Å2
ΔGint-48 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.669, 183.443, 41.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA5 - 180
211chain BB7 - 175

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Components

#1: Protein SMU-1 / Suppressor of Mec and Unc defects


Mass: 20802.508 Da / Num. of mol.: 2 / Fragment: NTR, UNP residues 2-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smu-1, CC4.3, CELE_CC4.3 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G5EEG7
#2: Protein Suppressor of Mec and Unc defects


Mass: 7011.264 Da / Num. of mol.: 2 / Fragment: UNP residues 163-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smu-2, CELE_Y49F6B.4, Y49F6B.4 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9N4U5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.1 M HEPES, pH 7.0, 0.02 M MgCl2, 19 % (w/v) polyacrilic acid 5,100
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979531, 0.979771, 0.977427
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9771
20.981
30.9795311
40.9797711
50.9774271
ReflectionResolution: 3.092→45.86 Å / Num. obs: 11889 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 102.6 Å2 / Rsym value: 0.103 / Net I/σ(I): 19.83
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.283 / Mean I/σ(I) obs: 2.04 / % possible all: 99.2

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
SHARPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 3.103→45.861 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.32 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3206 561 4.72 %Random selection
Rwork0.2831 11320 --
obs0.2849 11881 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.03 Å2 / Biso mean: 111.2601 Å2 / Biso min: 41.99 Å2
Refinement stepCycle: final / Resolution: 3.103→45.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 0 56 3186
Biso mean---91.93 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033174
X-RAY DIFFRACTIONf_angle_d0.7224293
X-RAY DIFFRACTIONf_chiral_restr0.028513
X-RAY DIFFRACTIONf_plane_restr0.002548
X-RAY DIFFRACTIONf_dihedral_angle_d14.0471203
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1407X-RAY DIFFRACTION6.296TORSIONAL
12B1407X-RAY DIFFRACTION6.296TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.103-3.41520.39021400.36642753289399
3.4152-3.90910.38061420.331527702912100
3.9091-4.92420.33881270.278628292956100
4.9242-45.86570.28061520.255829683120100

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