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- PDB-6yvh: CWC22-CWC27-EIF4A3 Complex -

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Basic information

Entry
Database: PDB / ID: 6yvh
TitleCWC22-CWC27-EIF4A3 Complex
Components
  • Eukaryotic initiation factor 4A-III
  • Pre-mRNA-splicing factor CWC22 homolog
  • Spliceosome-associated protein CWC27 homolog
KeywordsRNA BINDING PROTEIN / EJC Helicase
Function / homology
Function and homology information


negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of excitatory postsynaptic potential / Deadenylation of mRNA / embryonic cranial skeleton morphogenesis ...negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of excitatory postsynaptic potential / Deadenylation of mRNA / embryonic cranial skeleton morphogenesis / poly(A) binding / mRNA 3'-end processing / M-decay: degradation of maternal mRNAs by maternally stored factors / U2-type catalytic step 1 spliceosome / regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type catalytic step 2 spliceosome / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exploration behavior / associative learning / ribonucleoprotein complex binding / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to brain-derived neurotrophic factor stimulus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of translation / spliceosomal complex / mRNA splicing, via spliceosome / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / RNA stem-loop binding / rRNA processing / protein folding / RNA helicase activity / postsynapse / negative regulation of translation / nuclear speck / RNA helicase / neuronal cell body / mRNA binding / dendrite / nucleolus / glutamatergic synapse / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / : / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / : / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Eukaryotic initiation factor 4A-III / Spliceosome-associated protein CWC27 homolog / Pre-mRNA-splicing factor CWC22 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsBasquin, J. / Busetto, V. / LeHir, H. / Conti, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0023 France
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural and functional insights into CWC27/CWC22 heterodimer linking the exon junction complex to spliceosomes.
Authors: Busetto, V. / Barbosa, I. / Basquin, J. / Marquenet, E. / Hocq, R. / Hennion, M. / Paternina, J.A. / Namane, A. / Conti, E. / Bensaude, O. / Le Hir, H.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor CWC22 homolog
B: Pre-mRNA-splicing factor CWC22 homolog
C: Spliceosome-associated protein CWC27 homolog
D: Pre-mRNA-splicing factor CWC22 homolog
F: Pre-mRNA-splicing factor CWC22 homolog
H: Eukaryotic initiation factor 4A-III
J: Eukaryotic initiation factor 4A-III
K: Eukaryotic initiation factor 4A-III
L: Eukaryotic initiation factor 4A-III
I: Spliceosome-associated protein CWC27 homolog
E: Spliceosome-associated protein CWC27 homolog
G: Spliceosome-associated protein CWC27 homolog


Theoretical massNumber of molelcules
Total (without water)237,97712
Polymers237,97712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.255, 163.627, 181.131
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 132 through 133 or (resid 134...
d_2ens_1(chain "B" and (resid 132 through 133 or (resid 134...
d_3ens_1(chain "D" and (resid 132 through 138 or (resid 139...
d_4ens_1(chain "F" and (resid 132 through 133 or (resid 134...
d_1ens_2(chain "C" and (resid 378 through 394 or (resid 395...
d_2ens_2(chain "E" and (resid 378 through 387 or (resid 388...
d_3ens_2(chain "G" and (resid 378 through 380 or (resid 381...
d_4ens_2(chain "I" and (resid 378 through 387 or (resid 388...
d_1ens_3(chain "H" and ((resid 246 through 249 and (name N...
d_2ens_3(chain "J" and ((resid 246 through 249 and (name N...
d_3ens_3(chain "K" and ((resid 246 through 249 and (name N...
d_4ens_3(chain "L" and ((resid 246 through 249 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAARGA3 - 67
d_12ens_1VALLEUA71 - 276
d_21ens_1ALAARGC3 - 67
d_22ens_1VALLEUC71 - 276
d_31ens_1ALAARGD3 - 67
d_32ens_1VALLEUD71 - 276
d_41ens_1ALAARGE1 - 65
d_42ens_1VALLEUE69 - 274
d_11ens_2GLYGLUF1 - 28
d_12ens_2THRPHEF34 - 49
d_21ens_2GLYGLUG1 - 28
d_22ens_2THRPHEG34 - 49
d_31ens_2GLYPHEB1 - 44
d_41ens_2GLYGLUH1 - 28
d_42ens_2THRPHEH34 - 49
d_11ens_3LEULYSI1 - 42
d_12ens_3LYSTRPI44 - 92
d_13ens_3ASPILEI95 - 162
d_21ens_3LEULYSJ1 - 42
d_22ens_3LYSARGJ44 - 121
d_23ens_3ARGILEJ124 - 162
d_31ens_3LEULYSK1 - 42
d_32ens_3LYSTRPK46 - 94
d_33ens_3ASPARGK97 - 125
d_34ens_3ARGILEK128 - 166
d_41ens_3LEULYSL1 - 42
d_42ens_3LYSARGL44 - 121
d_43ens_3ARGILEL124 - 162

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.996311248058, -0.0641063736326, -0.057046208041), (-0.0639703085148, 0.11173508785, 0.991676897871), (-0.0571987466708, 0.991668111317, -0.115423829327)34.1746131554, 48.0889687745, -51.6378128261
2given(0.405281566248, 0.790535873332, 0.45912948613), (-0.27753123124, -0.372128640471, 0.88571817788), (0.871047224751, -0.48638802197, 0.0685815160087)76.7119521811, 2.29499338844, -44.2117826472
3given(0.333900339685, 0.810229617603, 0.481703778185), (0.904720450601, -0.418901576901, 0.0774749968358), (0.264559009341, 0.409938331495, -0.87290268355)42.0070432, -81.5799006748, -40.8028366945
4given(-0.470840145814, 0.516934532872, 0.714904361306), (0.24322164473, 0.855004326272, -0.45805112552), (-0.84802876639, -0.0417886441486, -0.528300028957)104.977002743, -70.9955419452, -40.7560555667
5given(-0.413180754835, 0.54031664279, 0.733034507618), (-0.88235310498, -0.0384340459638, -0.469015801698), (-0.22524356143, -0.840583576829, 0.492630275561)67.5785004979, -74.312950774, 33.1145923504
6given(-0.995631883092, -0.0662788773018, -0.065759134687), (-0.0727641996526, 0.109508167329, 0.991318986269), (-0.0585023471331, 0.991773699849, -0.113852552312)33.8622578176, 48.0801436623, -51.6845957958
7given(-0.995727897485, -0.0733142705197, -0.0561335185816), (-0.0657567646759, 0.136240361627, 0.988491078242), (-0.0648228514456, 0.987959301592, -0.140479238069)34.1131572322, 48.4686317985, -52.1371914512
8given(0.342486293965, 0.808172096164, 0.479125246077), (0.892045300492, -0.439779906154, 0.104157649804), (0.29488696193, 0.391728856641, -0.871544710591)41.3179130997, -81.0280499984, -41.8238164391
9given(0.411233290671, 0.786448806192, 0.46085296558), (-0.270067813166, -0.377760719334, 0.885641132299), (0.870603558996, -0.488666669794, 0.0570467255577)76.2504165006, 2.40866279043, -44.6583518973

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Components

#1: Protein
Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 33492.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CWC22, KIAA1604, NCM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HCG8
#2: Protein
Spliceosome-associated protein CWC27 homolog / Antigen NY-CO-10 / Probable inactive peptidyl-prolyl cis-trans isomerase CWC27 homolog / PPIase ...Antigen NY-CO-10 / Probable inactive peptidyl-prolyl cis-trans isomerase CWC27 homolog / PPIase CWC27 / Serologically defined colon cancer antigen 10


Mass: 6560.142 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CWC27, SDCCAG10, UNQ438/PRO871 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6UX04
#3: Protein
Eukaryotic initiation factor 4A-III / eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box ...eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Eukaryotic translation initiation factor 4A isoform 3 / Nuclear matrix protein 265 / hNMP 265


Mass: 19441.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A3, DDX48, KIAA0111 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38919, RNA helicase

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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: 4.71 Å3/Da / Density % sol: 73.88 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% (w/v) PEG20000, 50 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.19→94.69 Å / Num. obs: 143366 / % possible obs: 99.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 110.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.6
Reflection shellResolution: 3.19→3.36 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 97793 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
PHENIXdev_3758refinement
Aimlessdata reduction
XDSdata processing
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C9B

4c9b


Resolution: 3.19→94.69 Å / SU ML: 0.5768 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 31.3545
RfactorNum. reflection% reflection
Rfree0.2626 7473 5.21 %
Rwork0.2318 --
obs0.2334 143366 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 118.9 Å2
Refinement stepCycle: LAST / Resolution: 3.19→94.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14522 0 0 0 14522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003514778
X-RAY DIFFRACTIONf_angle_d0.709920120
X-RAY DIFFRACTIONf_chiral_restr0.04442407
X-RAY DIFFRACTIONf_plane_restr0.00432611
X-RAY DIFFRACTIONf_dihedral_angle_d7.48892035
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.579901313515
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.830529684923
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.759045964372
ens_2d_2FX-RAY DIFFRACTIONTorsion NCS0.664954597421
ens_2d_3FX-RAY DIFFRACTIONTorsion NCS1.29357685708
ens_2d_4FX-RAY DIFFRACTIONTorsion NCS0.570053463732
ens_3d_2IX-RAY DIFFRACTIONTorsion NCS0.605970256234
ens_3d_3IX-RAY DIFFRACTIONTorsion NCS0.842200962961
ens_3d_4IX-RAY DIFFRACTIONTorsion NCS0.738054345523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.230.48382330.43653777X-RAY DIFFRACTION83.07
3.23-3.270.43262080.38584567X-RAY DIFFRACTION99.96
3.27-3.310.36732190.36454569X-RAY DIFFRACTION99.94
3.31-3.350.36792660.36864566X-RAY DIFFRACTION99.94
3.35-3.390.39652240.36194551X-RAY DIFFRACTION99.87
3.39-3.440.42672460.37184591X-RAY DIFFRACTION99.9
3.44-3.490.41562330.35384569X-RAY DIFFRACTION99.94
3.49-3.540.35432530.33554588X-RAY DIFFRACTION99.94
3.54-3.590.36322990.31974489X-RAY DIFFRACTION99.9
3.6-3.650.36072370.2974560X-RAY DIFFRACTION99.92
3.65-3.720.30422280.27394569X-RAY DIFFRACTION99.96
3.72-3.780.32052720.274590X-RAY DIFFRACTION100
3.78-3.860.30892910.26564458X-RAY DIFFRACTION99.96
3.86-3.940.28673120.26924537X-RAY DIFFRACTION99.96
3.94-4.020.30362750.24774504X-RAY DIFFRACTION99.98
4.02-4.120.26362710.23324548X-RAY DIFFRACTION100
4.12-4.220.28022560.22344582X-RAY DIFFRACTION99.96
4.22-4.330.27322750.20714503X-RAY DIFFRACTION99.85
4.33-4.460.23052440.20344580X-RAY DIFFRACTION99.92
4.46-4.60.23492120.19364549X-RAY DIFFRACTION99.94
4.6-4.770.22562240.18594614X-RAY DIFFRACTION99.81
4.77-4.960.19822690.19044531X-RAY DIFFRACTION99.92
4.96-5.180.21032600.19214553X-RAY DIFFRACTION99.92
5.18-5.460.27182350.21864585X-RAY DIFFRACTION100
5.46-5.80.2872250.23864571X-RAY DIFFRACTION100
5.8-6.250.27272300.23924600X-RAY DIFFRACTION100
6.25-6.880.28322580.24714525X-RAY DIFFRACTION99.94
6.88-7.870.24912540.21344572X-RAY DIFFRACTION99.96
7.87-9.910.16752180.15794583X-RAY DIFFRACTION100
9.92-94.690.20462460.20854512X-RAY DIFFRACTION98.8
Refinement TLS params.Method: refined / Origin x: 34.7279692154 Å / Origin y: -15.635512523 Å / Origin z: -29.1025643033 Å
111213212223313233
T0.71248172549 Å2-0.0144997815353 Å2-0.0670277038799 Å2-0.902713636648 Å20.17367608368 Å2--0.849496761369 Å2
L-0.0306632096706 °2-0.348971354488 °20.161766066714 °2-0.34363500406 °2-0.19675353474 °2--0.268721944683 °2
S-0.0236736973986 Å °0.214878293386 Å °0.0961356861221 Å °0.0133872993541 Å °0.0353600740455 Å °-0.0222346501327 Å °-0.00250917648955 Å °-0.0467037934348 Å °-0.0038498460041 Å °
Refinement TLS groupSelection details: all

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