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- PDB-4u1c: Crystal structure of the eIF3a/eIF3c PCI-domain heterodimer -

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Basic information

Entry
Database: PDB / ID: 4u1c
TitleCrystal structure of the eIF3a/eIF3c PCI-domain heterodimer
Components
  • Eukaryotic translation initiation factor 3 subunit AEukaryotic initiation factor 3
  • Eukaryotic translation initiation factor 3 subunit CEukaryotic initiation factor 3
KeywordsTRANSLATION / translation initiation / eIF3 complex / PCI-domains
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / incipient cellular bud site / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex ...eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / incipient cellular bud site / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation 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 / translational initiation / translation initiation factor activity / cytoplasmic stress granule / mRNA binding / cytoplasm
Similarity search - Function
UVR domain / DNA Excision Repair, Uvrb; Chain A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Eukaryotic translation initiation factor 3 subunit A / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. ...UVR domain / DNA Excision Repair, Uvrb; Chain A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Eukaryotic translation initiation factor 3 subunit A / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsErzberger, J.P. / Schaefer, T. / Ban, N.
CitationJournal: Cell / Year: 2014
Title: Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex.
Authors: Jan P Erzberger / Florian Stengel / Riccardo Pellarin / Suyang Zhang / Tanja Schaefer / Christopher H S Aylett / Peter Cimermančič / Daniel Boehringer / Andrej Sali / Ruedi Aebersold / Nenad Ban /
Abstract: Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. We present X-ray structures of all major components of the minimal, ...Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. We present X-ray structures of all major components of the minimal, six-subunit Saccharomyces cerevisiae eIF3 core. These structures, together with electron microscopy reconstructions, cross-linking coupled to mass spectrometry, and integrative structure modeling, allowed us to position and orient all eIF3 components on the 40S⋅eIF1 complex, revealing an extended, modular arrangement of eIF3 subunits. Yeast eIF3 engages 40S in a clamp-like manner, fully encircling 40S to position key initiation factors on opposite ends of the mRNA channel, providing a platform for the recruitment, assembly, and regulation of the translation initiation machinery. The structures of eIF3 components reported here also have implications for understanding the architecture of the mammalian 43S preinitiation complex and the complex of eIF3, 40S, and the hepatitis C internal ribosomal entry site RNA.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Eukaryotic translation initiation factor 3 subunit C
A: Eukaryotic translation initiation factor 3 subunit A


Theoretical massNumber of molelcules
Total (without water)97,4912
Polymers97,4912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-11 kcal/mol
Surface area43340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.550, 155.550, 91.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit C / Eukaryotic initiation factor 3 / eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport ...eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport protein NIP1 / Translation initiation factor eIF3 / p93 subunit


Mass: 65808.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NIP1, YMR309C, YM9924.01C, YM9952.11C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32497
#2: Protein Eukaryotic translation initiation factor 3 subunit A / Eukaryotic initiation factor 3 / eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / ...eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / Translation initiation factor eIF3 / p110 subunit homolog


Mass: 31682.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RPG1, TIF32, YBR079C, YBR0734 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38249

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, KSCN, Bis-Tris-propane / PH range: 6.0-6.3

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 16368 / % possible obs: 99.9 % / Redundancy: 17.8 % / Biso Wilson estimate: 170 Å2 / Net I/σ(I): 27
Reflection shellResolution: 3.5→3.61 Å / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1539) / Classification: refinement
RefinementResolution: 3.5→44.903 Å / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2928 1628 9.96 %Random selection
Rwork0.2603 ---
obs0.2636 16350 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 174.8 Å2
Refinement stepCycle: LAST / Resolution: 3.5→44.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 0 0 6658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066788
X-RAY DIFFRACTIONf_angle_d1.0279190
X-RAY DIFFRACTIONf_dihedral_angle_d13.6492557
X-RAY DIFFRACTIONf_chiral_restr0.0371055
X-RAY DIFFRACTIONf_plane_restr0.0041166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-3.60310.45761350.39571227X-RAY DIFFRACTION100
3.6031-3.71940.39281300.3741181X-RAY DIFFRACTION100
3.7194-3.85220.40491380.3631224X-RAY DIFFRACTION100
3.8522-4.00640.46871360.35321225X-RAY DIFFRACTION100
4.0064-4.18860.38621350.32761204X-RAY DIFFRACTION100
4.1886-4.40920.35781300.29961213X-RAY DIFFRACTION100
4.4092-4.68520.29491360.28931212X-RAY DIFFRACTION100
4.6852-5.04650.35561350.28131222X-RAY DIFFRACTION100
5.0465-5.55350.38391360.31591224X-RAY DIFFRACTION100
5.5535-6.35520.39481390.3211236X-RAY DIFFRACTION100
6.3552-7.99950.31351350.26871243X-RAY DIFFRACTION100
7.9995-44.90710.18961430.19071311X-RAY DIFFRACTION100

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