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- PDB-1qva: YEAST INITIATION FACTOR 4A N-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1qva
TitleYEAST INITIATION FACTOR 4A N-TERMINAL DOMAIN
ComponentsINITIATION FACTOR 4A
KeywordsGENE REGULATION / RNA HELICASE / DEAD BOX / EIF4A
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / ATP-dependent activity, acting on RNA / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / ATP-dependent activity, acting on RNA / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation / translation initiation factor activity / cytoplasmic stress granule / RNA helicase activity / RNA helicase / ribosome / ATP hydrolysis activity / RNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / 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 / 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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase eIF4A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsJohnson, E.R. / McKay, D.B.
CitationJournal: RNA / Year: 1999
Title: Crystallographic structure of the amino terminal domain of yeast initiation factor 4A, a representative DEAD-box RNA helicase
Authors: Johnson, E.R. / McKay, D.B.
History
DepositionJul 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: INITIATION FACTOR 4A


Theoretical massNumber of molelcules
Total (without water)24,9501
Polymers24,9501
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.800, 74.300, 81.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein INITIATION FACTOR 4A / EIF-4A / STIMULATOR FACTOR I 37 / KD COMPONENT


Mass: 24949.701 Da / Num. of mol.: 1 / Fragment: residues 2-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P10081
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: POLYETHYLENE GLYCOL, POTASSIUM ACETATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %mPEG50001reservoir
2100 mM1reservoirKOAc
350 mMCHES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9999
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 8094 / Num. obs: 8094 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.1
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.146 / Num. unique all: 1095 / % possible all: 78.8
Reflection
*PLUS
Num. obs: 8026 / % possible obs: 93.8 % / Num. measured all: 29694
Reflection shell
*PLUS
% possible obs: 72.7 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
CNSrefinement
QUANTUMIV CCD SOFTWAREdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.5→40 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 415484.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh & Huber, Konnert & Hendrickson
Details: The sidechains of the following residues were not observed in the electron density and are modeled as ALA: GLN 11, ARG 137, GLN 154, ARG 156, ARG 157, ARG 159
RfactorNum. reflection% reflectionSelection details
Rfree0.274 830 10.3 %RANDOM
Rwork0.223 ---
all0.228 8026 --
obs0.223 8026 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.24 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1--11.67 Å20 Å20 Å2
2---5.77 Å20 Å2
3---17.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 55 1698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 114 10.7 %
Rwork0.267 952 -
obs--76.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TOPPAR_EJ:PROTEIN_REP.PARTOPPAR_EJ:PROTEIN.TOP
X-RAY DIFFRACTION2TOPPAR_EJ:WATER_REP.PARAMTOPPAR_EJ:WATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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