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- PDB-5en7: Crystal structure of the Smu1-RED complex (native) of Caenorhabdi... -

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Basic information

Entry
Database: PDB / ID: 5en7
TitleCrystal structure of the Smu1-RED complex (native) of Caenorhabditis elegans.
Components
  • SMU-1
  • Suppressor of Mec and Unc defects
KeywordsSPLICING / LisH motif / CTLH / dimer / heterotetramer
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.936 Å
AuthorsUlrich, A.K.C. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWA1126/7-1 Germany
CitationJournal: to be published
Title: splicing factor
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
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,6928
Polymers110,6928
Non-polymers00
Water2,540141
1
A: SMU-1
B: Suppressor of Mec and Unc defects
C: SMU-1
D: Suppressor of Mec and Unc defects


Theoretical massNumber of molelcules
Total (without water)55,3464
Polymers55,3464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-46 kcal/mol
Surface area22140 Å2
MethodPISA
2
E: SMU-1
F: Suppressor of Mec and Unc defects
G: SMU-1
H: Suppressor of Mec and Unc defects


Theoretical massNumber of molelcules
Total (without water)55,3464
Polymers55,3464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-51 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.322, 41.036, 126.382
Angle α, β, γ (deg.)90.000, 95.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain C and segid C
31chain E and segid E
41chain G and segid G
12chain B and segid B
22chain D and segid D
32chain F and segid F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain C and segid CC0
311chain E and segid EE0
411chain G and segid GG0
112chain B and segid BB0
212chain D and segid DD0
312chain F and segid FF0

NCS ensembles :
ID
1
2

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Components

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


Mass: 20708.719 Da / Num. of mol.: 4 / 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: 6964.369 Da / Num. of mol.: 4 / 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.: 141 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.1 M HEPES, pH 7.5, 0.02 M MgCl2, 22 % [w/v] polyacrilic acid 5,100
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.936→46.16 Å / Num. obs: 26994 / % possible obs: 98.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 62.7 Å2 / CC1/2: 0.995 / Rsym value: 0.124 / Net I/σ(I): 10.6
Reflection shellResolution: 2.94→3.11 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.4 / % possible all: 92.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5en6

5en6


Resolution: 2.936→46.156 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 1350 5 %Random selection
Rwork0.2215 25634 --
obs0.2239 26984 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.65 Å2 / Biso mean: 67.6457 Å2 / Biso min: 17.2 Å2
Refinement stepCycle: final / Resolution: 2.936→46.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 0 141 6461
Biso mean---53.71 -
Num. residues----785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056411
X-RAY DIFFRACTIONf_angle_d0.8988670
X-RAY DIFFRACTIONf_chiral_restr0.0381034
X-RAY DIFFRACTIONf_plane_restr0.0041106
X-RAY DIFFRACTIONf_dihedral_angle_d14.5612457
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3414X-RAY DIFFRACTION12.234TORSIONAL
12C3414X-RAY DIFFRACTION12.234TORSIONAL
13E3414X-RAY DIFFRACTION12.234TORSIONAL
14G3414X-RAY DIFFRACTION12.234TORSIONAL
21B217X-RAY DIFFRACTION12.234TORSIONAL
22D217X-RAY DIFFRACTION12.234TORSIONAL
23F217X-RAY DIFFRACTION12.234TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9361-3.0410.38961170.34742216233388
3.041-3.16280.3371370.30126022739100
3.1628-3.30670.36571320.26762521265399
3.3067-3.4810.32311360.260625822718100
3.481-3.6990.26161380.223826102748100
3.699-3.98440.281340.20642540267499
3.9844-4.38510.26361350.1852568270399
4.3851-5.0190.20541380.183326252763100
5.019-6.32080.26361380.230426342772100
6.3208-46.16180.23711450.2042736288199

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