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

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Basic information

Entry
Database: PDB / ID: 2vsx
TitleCrystal Structure of a Translation Initiation Complex
Components
  • ATP-DEPENDENT RNA HELICASE EIF4A
  • EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150
KeywordsTRANSLATION/HYDROLASE / ACETYLATION / ATP-BINDING / PHOSPHOPROTEIN / PROTEIN BIOSYNTHESIS / TRANSLATION REGULATION / TRANSLATION INITIATION / INITIATION FACTOR / NUCLEOTIDE-BINDING / HELICASE / HYDROLASE / CYTOPLASM / RNA-BINDING / TRANSLATION-HYDROLASE complex
Function / homology
Function and homology information


Deadenylation of mRNA / 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 / 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 ...Deadenylation of mRNA / 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 / 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 / ATPase activator activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / stress granule assembly / translational initiation / translation initiation factor activity / ribosomal large subunit biogenesis / molecular condensate scaffold activity / P-body / 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. / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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 30, 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 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 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
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-24.5 kcal/mol
Surface area67290 Å2
MethodPQS
2
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.920, 111.360, 111.280
Angle α, β, γ (deg.)90.00, 99.71, 90.00
Int Tables number4
Space group name H-MP1211
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 / P37EIF4A


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 / / EIF4F P150 / EIF-4F P150 / EIF4G1 / MRNA CAP-BINDING PROTEIN COMPLEX SUBUNIT P150 / EIF4G


Mass: 32360.195 Da / Num. of mol.: 2 / Fragment: MIDDLE DOMAIN, 4A-BINDING, RESIDUES 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 / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7.2
Details: 0.2 M TARTRATE, 20 % PEG 3350, PH 7.2, 4 DEG C, 10 ,MM AMP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Date: Mar 15, 2002 / Details: OSMICS MIRROR
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 40597 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 37.35 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1QDE, 1FUK, 1HU3

1qde

1fuk

1hu3


Resolution: 2.8→33.21 Å / SU ML: 0.41 / Phase error: 35.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 1668 4.1 %
Rwork0.252 --
obs0.2535 40575 99.8 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.709 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1--11.4693 Å20 Å25.8803 Å2
2---18.4761 Å20 Å2
3----5.5536 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9577 0 46 0 9623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039768
X-RAY DIFFRACTIONf_angle_d0.59413188
X-RAY DIFFRACTIONf_dihedral_angle_d11.8913630
X-RAY DIFFRACTIONf_chiral_restr0.0481544
X-RAY DIFFRACTIONf_plane_restr0.0021668
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2907X-RAY DIFFRACTIONPOSITIONAL
12B2907X-RAY DIFFRACTIONPOSITIONAL0.015
21E1807X-RAY DIFFRACTIONPOSITIONAL
22F1807X-RAY DIFFRACTIONPOSITIONAL0.018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8031-2.88560.39131440.3393004X-RAY DIFFRACTION93
2.8856-2.97870.32041390.32163236X-RAY DIFFRACTION100
2.9787-3.08510.38661480.31333233X-RAY DIFFRACTION100
3.0851-3.20850.38191270.30113252X-RAY DIFFRACTION100
3.2085-3.35440.28571300.28733288X-RAY DIFFRACTION100
3.3544-3.5310.29691420.26773214X-RAY DIFFRACTION100
3.531-3.7520.31481260.26163278X-RAY DIFFRACTION100
3.752-4.04120.2991370.24333266X-RAY DIFFRACTION100
4.0412-4.4470.25911430.20993262X-RAY DIFFRACTION100
4.447-5.08860.24241240.19273283X-RAY DIFFRACTION100
5.0886-6.40350.27081550.23973259X-RAY DIFFRACTION100
6.4035-33.20820.19951530.21073332X-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)
10.8737-0.4733-1.0872.28250.61332.84490.15080.50810.077-0.0190.17310.0302-0.084-0.1544-0.07640.17460.05720.04870.31260.13420.105339.7948-13.2184-8.6602
2-0.8124-0.40870.24830.9968-0.23824.2492-0.17740.1087-0.0635-0.2217-0.10320.42560.3349-0.05690.18030.13210.02710.03520.44340.13080.261210.8883-26.104211.6339
31.5207-0.9827-1.40751.40860.46574.9386-0.6303-0.5252-0.8359-0.4367-0.3564-0.38640.40251.81160.80590.48830.26270.24880.75890.31040.500317.1803-34.555717.6494
42.5970.7910.20752.2586-0.08790.7170.10630.9072-0.1201-0.5937-0.0403-0.03190.04690.35860.44610.1682-0.0180.08810.44790.1152-0-0.0706-13.1924-18.4464
50.61550.295-0.42831.23920.78661.45340.06140.50120.0821-0.0909-0.26720.0034-0.0043-0.2520.17710.32040.1078-0.08181.08950.02540.233828.8795-25.8074-38.8387
60.54560.0604-0.81771.15440.81630.55110.06090.60680.1502-0.2471-0.80470.4206-0.3299-1.71540.63860.49720.0369-0.09021.4372-0.15630.259322.6093-34.1955-44.9643
70.6243-0.23930.54291.43860.08250.9557-0.0719-0.40810.00230.0793-0.1196-0.18090.05160.08620.14490.288-0.03340.0240.46070.09350.20851.5331-9.178225.9028
83.20180.658-0.09880.3369-0.56890.05080.293-0.8979-0.25010.2639-0.19270.0243-0.0653-0.0702-0.06190.31080.00330.03470.39370.01850.116521.97815.136325.1397
91.0249-0.55730.09440.4221-0.1822-0.7743-0.37240.69250.28030.05170.1206-0.14970.31570.19540.21570.4802-0.02440.0771.00450.19750.184338.0095-8.6132-53.1624
102.30780.2955-1.85060.2302-0.47232.0480.71790.58271.10820.405-0.159-0.0606-0.9211-0.4895-0.39190.6401-0.00320.17511.06820.47890.624817.42275.4711-52.6354
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 577:679
8X-RAY DIFFRACTION8CHAIN E AND RESID 680:853
9X-RAY DIFFRACTION9CHAIN F AND RESID 577:679
10X-RAY DIFFRACTION10CHAIN F AND RESID 680:853

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