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- PDB-2vso: Crystal Structure of a Translation Initiation Complex -

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Basic information

Entry
Database: PDB / ID: 2vso
TitleCrystal Structure of a Translation Initiation Complex
Components
  • ATP-DEPENDENT RNA HELICASE EIF4A
  • EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150
KeywordsHYDROLASE/TRANSLATION / ACETYLATION / ATP-BINDING / PHOSPHOPROTEIN / PROTEIN BIOSYNTHESIS / TRANSLATION REGULATION / TRANSLATION INITIATION / INITIATION FACTOR / NUCLEOTIDE-BINDING / HELICASE / HYDROLASE / CYTOPLASM / RNA-BINDING / HYDROLASE-TRANSLATION complex
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 / regulation of protein metabolic process / ATP-dependent activity, acting on RNA / positive regulation of endoplasmic reticulum unfolded protein response / mTORC1-mediated signalling / regulation of 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 / Deadenylation of mRNA / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / regulation of protein metabolic process / ATP-dependent activity, acting on RNA / positive regulation of endoplasmic reticulum unfolded protein response / mTORC1-mediated signalling / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / cellular response to glucose starvation / stress granule assembly / translation initiation factor activity / ribosomal large subunit biogenesis / translational initiation / P-body / molecular condensate scaffold activity / cytoplasmic stress granule / RNA helicase activity / ribosome / RNA helicase / mRNA binding / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / Initiation factor 4G / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / DEAD-box subfamily ATP-dependent helicases signature. ...Eukaryotic translation initiation factor 4G1, eIF4E-binding domain / eIF4G, eIF4e-binding domain superfamily / Eukaryotic translation initiation factor 4G1 / ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / Initiation factor 4G / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / 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
ADENOSINE MONOPHOSPHATE / ATP-dependent RNA helicase eIF4A / Eukaryotic initiation factor 4F subunit p150
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchutz, P. / Bumann, M. / Oberholzer, A.E. / Bieniossek, C. / Altmann, M. / Trachsel, H. / Baumann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal Structure of the Yeast Eif4A-Eif4G Complex: An RNA-Helicase Controlled by Protein-Protein Interactions.
Authors: Schutz, P. / Bumann, M. / Oberholzer, A.E. / Bieniossek, C. / Trachsel, H. / Altmann, M. / Baumann, U.
History
DepositionApr 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT RNA HELICASE EIF4A
B: ATP-DEPENDENT RNA HELICASE EIF4A
E: EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150
F: EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,9076
Polymers154,2124
Non-polymers6942
Water1,36976
1
A: ATP-DEPENDENT RNA HELICASE EIF4A
E: EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4533
Polymers77,1062
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-13.5 kcal/mol
Surface area34940 Å2
MethodPQS
2
B: ATP-DEPENDENT RNA HELICASE EIF4A
F: EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4533
Polymers77,1062
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-12.7 kcal/mol
Surface area34810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)69.260, 69.800, 101.970
Angle α, β, γ (deg.)91.70, 102.01, 115.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 12:125 OR RESSEQ 136:350 OR RESSEQ 357:393 )
211CHAIN B AND (RESSEQ 12:125 OR RESSEQ 136:350 OR RESSEQ 357:393 )
112CHAIN E AND (RESSEQ 598:685 OR RESSEQ 689:716 OR RESSEQ...
212CHAIN F AND (RESSEQ 598:685 OR RESSEQ 689:716 OR RESSEQ...

NCS ensembles :
ID
1
2

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Components

#1: Protein ATP-DEPENDENT RNA HELICASE EIF4A / EUKARYOTIC INITIATION FACTOR 4A / EIF-4A / TRANSLATION INITIATION FACTOR 1/2 / STIMULATOR FACTOR I ...EUKARYOTIC INITIATION FACTOR 4A / EIF-4A / TRANSLATION INITIATION FACTOR 1/2 / STIMULATOR FACTOR I 37 KDA COMPONENT / P37 / EIF4A


Mass: 44745.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA
References: UniProt: P10081, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150 / EIF4G / EIF4F P150 / EIF-4F P150 / EIF4G1 / MRNA CAP-BINDING PROTEIN COMPLEX SUBUNIT P150


Mass: 32360.195 Da / Num. of mol.: 2 / Fragment: MIDDLE DOMAIN, 4A-BINDING, 572-854
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39935
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7 / Details: 0.2 M TARTRATE, 20% PEG3350, PH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 1, 2006 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 48104 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 37.35 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 14.6
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1QDE, 1FUK, 1HU3

1qde

1fuk

1hu3


Resolution: 2.6→48.012 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 29.17 / Stereochemistry target values: ML
Details: DISORDERED SIDE CHAINS WERE FREQUENTLY MODELED AS ALANINE.
RfactorNum. reflection% reflection
Rfree0.2601 1314 2.7 %
Rwork0.2142 --
obs0.2154 48580 94.18 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.328 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.6018 Å2-8.3964 Å2-10.9456 Å2
2---9.977 Å2-13.8083 Å2
3---1.2734 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9572 0 46 76 9694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089762
X-RAY DIFFRACTIONf_angle_d1.08813180
X-RAY DIFFRACTIONf_dihedral_angle_d15.3953628
X-RAY DIFFRACTIONf_chiral_restr0.0781543
X-RAY DIFFRACTIONf_plane_restr0.0041667
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2907X-RAY DIFFRACTIONPOSITIONAL
12B2907X-RAY DIFFRACTIONPOSITIONAL0.033
21E1807X-RAY DIFFRACTIONPOSITIONAL
22F1807X-RAY DIFFRACTIONPOSITIONAL0.034
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)
11.65140.81490.38291.96680.79611.89130.1086-0.1209-0.1113-0.09040.05550.03410.2608-0.3777-0.11320.2867-0.09690.01430.4030.20730.098620.037-1.5571-3.9648
20.53070.4686-0.69631.31230.55073.13390.14240.3293-0.3627-0.2713-0.0052-0.03590.02070.4384-0.10490.29870.26180.02250.70630.01720.207-9.06940.7901-27.9611
32.78740.64870.59991.14711.53432.8194-0.25970.8938-0.1341-0.43820.78970.0213-1.04861.1728-0.50810.68090.01610.10111.2129-0.09910.3388-2.70595.5963-37.1023
42.2444-0.81420.72242.17260.32822.68610.3099-0.5098-0.11630.5834-0.0708-0.10230.2921-0.11520.3710.2178-0.0004-0.03910.28020.1926-0.0231-20.0922.76284.6734
51.2113-0.86330.1631.58690.71421.6749-0.1726-0.00430.0391-0.1479-0.0086-0.0921-0.2070.28840.13850.373-0.07880.09530.74020.0670.26628.960923.352717.306
62.6358-0.90080.07212.19330.72062.6709-0.4322-0.0874-0.0378-0.0991-0.46880.2515-0.511-0.45560.63250.47810.1346-0.10490.769-0.02930.42852.578433.53818.9729
70.8819-0.56510.20031.0140.06210.9859-0.34420.18190.249-0.14170.0360.1863-0.4784-0.34950.21830.43560.1438-0.10820.48440.00840.2815-18.0436-20.7781-33.4714
83.0135-0.49450.91280.6621-0.42951.63590.07360.3312-0.3975-0.12490.01790.04820.1290.0702-0.06350.38490.00820.02320.32590.03110.21862.3838-33.3108-26.3028
91.40570.2719-0.18911.804-1.16640.3486-0.0863-0.30870.26310.1798-0.0253-0.18560.00970.22730.08060.26880.04660.04730.66730.06650.088218.17314.593237.8409
101.96410.54920.91161.27050.35152.4720.4478-0.5074-0.43260.2655-0.1964-0.00471.0143-0.4495-0.22150.7187-0.106-0.05850.83720.17840.1434-2.47551.805243.6655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 11:224
2X-RAY DIFFRACTION2CHAIN A AND RESID 225:319
3X-RAY DIFFRACTION3CHAIN A AND RESID 320:391
4X-RAY DIFFRACTION4CHAIN B AND RESID 11:224
5X-RAY DIFFRACTION5CHAIN B AND RESID 225:319
6X-RAY DIFFRACTION6CHAIN B AND RESID 320:391
7X-RAY DIFFRACTION7CHAIN E AND RESID 576:679
8X-RAY DIFFRACTION8CHAIN E AND RESID 680:853
9X-RAY DIFFRACTION9CHAIN F AND RESID 576:679
10X-RAY DIFFRACTION10CHAIN F AND RESID 680:853

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