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- PDB-3zwl: Structure of eukaryotic translation initiation factor eIF3i compl... -

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Basic information

Entry
Database: PDB / ID: 3zwl
TitleStructure of eukaryotic translation initiation factor eIF3i complex with eIF3b C-terminus (655-700)
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
KeywordsTRANSLATION
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation ...eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding / translation initiation factor activity / translational initiation / cytoplasmic stress granule / RNA binding / identical protein binding
Similarity search - Function
EIF3I / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / RNA recognition motif ...EIF3I / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / WD domain, G-beta repeat / Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsDaujotyte, D. / Lukavsky, P.J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural Analysis of an Eif3 Subcomplex Reveals Conserved Interactions Required for a Stable and Proper Translation Pre-Initiation Complex Assembly.
Authors: Herrmannova, A. / Daujotyte, D. / Yang, J.C. / Cuchalova, L. / Gorrec, F. / Wagner, S. / Danyi, I. / Lukavsky, P.J. / Shivaya Valasek, L.
History
DepositionAug 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Apr 18, 2012Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
D: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B


Theoretical massNumber of molelcules
Total (without water)94,7324
Polymers94,7324
Non-polymers00
Water4,252236
1
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B


Theoretical massNumber of molelcules
Total (without water)47,3662
Polymers47,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-16 kcal/mol
Surface area17760 Å2
MethodPISA
2
D: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B


Theoretical massNumber of molelcules
Total (without water)47,3662
Polymers47,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15.1 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.469, 126.469, 105.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I / EIF3I / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 39 KDA SUBUNIT / EIF-3 39 KDA SUBUNIT / EIF3 P39 / TIF34


Mass: 41302.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40217
#2: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B / EIF3B / CELL CYCLE REGULATION AND TRANSLATION INITIATION PROTEIN / EUKARYOTIC TRANSLATION ...EIF3B / CELL CYCLE REGULATION AND TRANSLATION INITIATION PROTEIN / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 90 KDA SUBUNIT / EIF3 P90 / TRANSLATION INITIATION FACTOR EIF3 P90 SUBUNIT / PRT1


Mass: 6062.861 Da / Num. of mol.: 2 / Fragment: RESIDUES 693-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06103
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS TAG AND TEV PROTEASE CLEAVAGE SITE ARE PRESENT. THREE RESIDUES GSH FROM TEV PROTEASE ...N-TERMINAL HIS TAG AND TEV PROTEASE CLEAVAGE SITE ARE PRESENT. THREE RESIDUES GSH FROM TEV PROTEASE CLEAVAGE SITE ARE PRESENT.

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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: 2.7 Å3/Da / Density % sol: 54.45 % / Description: NONE
Crystal growpH: 8.8
Details: 0.1 M TRIS PH 8.8, 0.1 M LI2SO4, 30% PEG4000, 8% DIAMINOPENTANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→54.7 Å / Num. obs: 49844 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
BUCCANEERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.2→109.53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.545 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES B260-271 ARE OMITTED FROM THE PDB FILE DUE TO THE LACK OF ELECTRON DENSITY AROUND THEM.
RfactorNum. reflection% reflectionSelection details
Rfree0.24706 2524 5.1 %RANDOM
Rwork0.18871 ---
obs0.19166 47261 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→109.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6145 0 0 236 6381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.9428498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2165764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9524.751301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4051522
X-RAY DIFFRACTIONr_chiral_restr0.1280.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214764
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2631.53807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43426150
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.77532483
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2034.52348
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 195 -
Rwork0.251 3454 -
obs--99.97 %

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