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- PDB-1fuu: YEAST INITIATION FACTOR 4A -

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Basic information

Entry
Database: PDB / ID: 1fuu
TitleYEAST INITIATION FACTOR 4A
ComponentsYEAST INITIATION FACTOR 4A
KeywordsTRANSLATION / IF4A / HELICASE / DEAD-BOX PROTEIN
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 / Deadenylation of mRNA / 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 ...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 / Deadenylation of mRNA / 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 / translation initiation factor activity / translational initiation / 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 domain / DEAD/DEAH box helicase / 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 domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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
AuthorsCaruthers, J.M. / Johnson, E.R. / McKay, D.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase.
Authors: Caruthers, J.M. / Johnson, E.R. / McKay, D.B.
History
DepositionSep 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YEAST INITIATION FACTOR 4A
B: YEAST INITIATION FACTOR 4A


Theoretical massNumber of molelcules
Total (without water)90,2612
Polymers90,2612
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.800, 71.200, 73.200
Angle α, β, γ (deg.)94.00, 89.60, 101.00
Int Tables number1
Space group name H-MP1
Detailsthe biological assembly is a dumbell of two domains connected by an eleven-residue linker

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Components

#1: Protein YEAST INITIATION FACTOR 4A / EUKARYOTIC INITIATION FACTOR 4A


Mass: 45130.637 Da / Num. of mol.: 2 / Fragment: MRNA HELICASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P10081
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: CHAPS, guanidinium, KOAc, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %mPEG55011
21 mM11ZnSO4
3100 mMMES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.92
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 48114 / Num. obs: 16117 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.99 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.079
Reflection shellHighest resolution: 2.5 Å
Reflection
*PLUS
% possible obs: 92 % / Num. measured all: 53337 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 80.4 % / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.5→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2726 21283 RANDOM
Rwork0.2435 --
all0.279 26525 -
obs0.252 22369 -
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 0 146 4800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_torsion_impr_deg0.86
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.273 / Rfactor Rwork: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS

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