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- PDB-4c9b: Crystal structure of eIF4AIII-CWC22 complex -

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Basic information

Entry
Database: PDB / ID: 4c9b
TitleCrystal structure of eIF4AIII-CWC22 complex
Components
  • EUKARYOTIC INITIATION FACTOR 4A-III
  • PRE-MRNA-SPLICING FACTOR CWC22 HOMOLOG
KeywordsSPLICING / DEAD-BOX HELICASE / NMD / MRNP
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 / 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 / selenocysteine insertion sequence binding / poly(A) binding ...negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / 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 / selenocysteine insertion sequence binding / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-end processing / U2-type catalytic step 1 spliceosome / embryonic cranial skeleton morphogenesis / 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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RNA Polymerase II Transcription Termination / exploration behavior / associative learning / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / ribonucleoprotein complex binding / cellular response to brain-derived neurotrophic factor stimulus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of translation / spliceosomal complex / response to organic cyclic compound / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / RNA stem-loop binding / rRNA processing / postsynapse / RNA helicase activity / negative regulation of translation / RNA helicase / nuclear speck / mRNA binding / neuronal cell body / glutamatergic synapse / dendrite / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / 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. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Eukaryotic initiation factor 4A-III / Pre-mRNA-splicing factor CWC22 homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBuchwald, G. / Schuessler, S. / Basquin, C. / LeHir, H. / Conti, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal Structure of the Human Eif4Aiii-Cwc22 Complex Shows How a Dead-Box Protein is Inhibited by a Mif4G Domain
Authors: Buchwald, G. / Schuessler, S. / Basquin, C. / Le Hir, H. / Conti, E.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EUKARYOTIC INITIATION FACTOR 4A-III
B: PRE-MRNA-SPLICING FACTOR CWC22 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,36012
Polymers80,4362
Non-polymers92410
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-19.6 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.290, 108.720, 61.370
Angle α, β, γ (deg.)90.00, 99.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EUKARYOTIC INITIATION FACTOR 4A-III / EIF-4A-III / EIF4A-III / ATP-DEPENDENT RNA HELICASE DDX48 / ATP-DEPENDENT RNA HELICASE EIF4A-3 / ...EIF-4A-III / 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 / NMP 265 / HNMP 265 / EUKARYOTIC INITIATION FACTOR 4A-III / N-TERMINALLY PROCESSED


Mass: 46930.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P38919, RNA helicase
#2: Protein PRE-MRNA-SPLICING FACTOR CWC22 HOMOLOG / PRE-MRNA-SPLICING FACTOR CWC22 / NUCAMPHOLIN HOMOLOG / FSAPB


Mass: 33505.039 Da / Num. of mol.: 1 / Fragment: MIF4G DOMAIN, RESIDUES 116-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q9HCG8
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.3 Å3/Da / Density % sol: 46.58 % / Description: NONE
Crystal growDetails: 12% PEG 20000, 0.1 M NA-K-PHOSPHATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2012 / Details: BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2→55.4 Å / Num. obs: 48938 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 26.25 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.68
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.17 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→55.445 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 2447 5 %
Rwork0.2017 --
obs0.2035 48938 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.8 Å2
Refinement stepCycle: LAST / Resolution: 2→55.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 59 298 5640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065478
X-RAY DIFFRACTIONf_angle_d0.8727396
X-RAY DIFFRACTIONf_dihedral_angle_d12.0792103
X-RAY DIFFRACTIONf_chiral_restr0.059851
X-RAY DIFFRACTIONf_plane_restr0.003947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04090.33721420.28152712X-RAY DIFFRACTION99
2.0409-2.08530.28731430.25932718X-RAY DIFFRACTION100
2.0853-2.13380.30131420.24622710X-RAY DIFFRACTION100
2.1338-2.18720.29261420.22712739X-RAY DIFFRACTION100
2.1872-2.24630.30241450.22392737X-RAY DIFFRACTION100
2.2463-2.31240.26771440.21742742X-RAY DIFFRACTION100
2.3124-2.38710.24811410.20562683X-RAY DIFFRACTION100
2.3871-2.47240.27341450.20642745X-RAY DIFFRACTION100
2.4724-2.57140.21961450.20042745X-RAY DIFFRACTION100
2.5714-2.68840.25791440.19782736X-RAY DIFFRACTION100
2.6884-2.83010.24351440.20672726X-RAY DIFFRACTION100
2.8301-3.00740.22121440.19382747X-RAY DIFFRACTION100
3.0074-3.23960.25551440.20432719X-RAY DIFFRACTION100
3.2396-3.56560.23011440.19062732X-RAY DIFFRACTION100
3.5656-4.08140.20331450.18492757X-RAY DIFFRACTION100
4.0814-5.14150.21161450.17642761X-RAY DIFFRACTION100
5.1415-55.4660.20241480.20232782X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8558-0.17130.69392.8501-0.41462.0469-0.0346-0.00650.00180.14510.01570.01090.05620.01850.02320.42480.02420.03170.1900.174430.050164.757244.4851
22.80350.1503-0.46592.45810.50471.6581-0.00770.2103-0.3166-0.1996-0.00560.04110.15920.03740.01090.6933-0.001-0.01250.2563-0.00590.21473.796883.331415.8736
31.546-0.10970.75341.2363-0.09011.99750.0122-0.0520.0461-0.09070.02090.0927-0.00730.0384-0.03810.5268-0.00980.03990.1875-0.02160.1808-2.166792.025143.9919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 21 THROUGH 250)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 251 THROUGH 411)
3X-RAY DIFFRACTION3CHAIN B AND (RESID 123 THROUGH 406)

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