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- PDB-4u1d: Structure of the PCI domain of translation initiation factor eIF3a -

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Basic information

Entry
Database: PDB / ID: 4u1d
TitleStructure of the PCI domain of translation initiation factor eIF3a
ComponentsEukaryotic translation initiation factor 3 subunit AEukaryotic initiation factor 3
KeywordsTRANSLATION / translation initiation / eIF3 complex / PCI domain
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 / translational initiation / translation initiation factor activity / cytoplasmic stress granule / mRNA binding / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit A / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / Proteasome component (PCI) domain / PCI domain profile.
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 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 A
B: Eukaryotic translation initiation factor 3 subunit A
A: Eukaryotic translation initiation factor 3 subunit A


Theoretical massNumber of molelcules
Total (without water)171,0383
Polymers171,0383
Non-polymers00
Water0
1
C: Eukaryotic translation initiation factor 3 subunit A


Theoretical massNumber of molelcules
Total (without water)57,0131
Polymers57,0131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 3 subunit A


Theoretical massNumber of molelcules
Total (without water)57,0131
Polymers57,0131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Eukaryotic translation initiation factor 3 subunit A


Theoretical massNumber of molelcules
Total (without water)57,0131
Polymers57,0131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)242.530, 158.270, 93.740
Angle α, β, γ (deg.)90.00, 104.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: 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: 57012.719 Da / Num. of mol.: 3
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: 5.1 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, KSCN, Bis-Tris-propane / PH range: 6.8-8.8

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.294→40 Å / Num. obs: 48944 / % possible obs: 94.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 112 Å2 / Net I/σ(I): 11.14
Reflection shellResolution: 3.294→3.5 Å / Mean I/σ(I) obs: 1.53 / % possible all: 92.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementResolution: 3.3→39.568 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 2446 5.01 %Random selection
Rwork0.1703 ---
obs0.1719 48847 94.22 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 118.1 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11013 0 0 0 11013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511230
X-RAY DIFFRACTIONf_angle_d0.91115179
X-RAY DIFFRACTIONf_dihedral_angle_d12.6264218
X-RAY DIFFRACTIONf_chiral_restr0.0541731
X-RAY DIFFRACTIONf_plane_restr0.0041905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2943-3.36150.34031350.33952553X-RAY DIFFRACTION88
3.3615-3.43450.29531430.29612717X-RAY DIFFRACTION96
3.4345-3.51440.27861440.26932737X-RAY DIFFRACTION95
3.5144-3.60220.2991450.25832744X-RAY DIFFRACTION94
3.6022-3.69950.24791400.25032677X-RAY DIFFRACTION93
3.6995-3.80830.26071400.21992638X-RAY DIFFRACTION91
3.8083-3.93110.23161470.19852794X-RAY DIFFRACTION97
3.9311-4.07150.21991490.18432819X-RAY DIFFRACTION97
4.0715-4.23430.18211480.15262799X-RAY DIFFRACTION97
4.2343-4.42680.16781470.13862812X-RAY DIFFRACTION98
4.4268-4.65980.16341480.13452794X-RAY DIFFRACTION96
4.6598-4.95130.18341450.12922754X-RAY DIFFRACTION95
4.9513-5.33270.20281420.1412686X-RAY DIFFRACTION93
5.3327-5.86780.22371410.16372689X-RAY DIFFRACTION92
5.8678-6.71340.20921480.17512797X-RAY DIFFRACTION96
6.7134-8.44460.19781420.15592696X-RAY DIFFRACTION93
8.4446-39.57030.16321420.14562695X-RAY DIFFRACTION91
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)
10.220.37630.60420.50240.66590.31750.21820.25990.17510.02550.0059-0.7440.0419-0.277-0.00170.74690.1323-0.05290.8660.24971.351957.8259114.943282.7074
20.1865-0.0665-0.54031.15080.4632-0.19750.16520.08420.3635-0.08750.0371-0.26770.232-0.223-0.00010.79290.1564-0.10410.97230.1410.858153.525684.430870.0262
31.05220.5137-0.57181.60430.01140.73510.14410.3257-0.1357-0.1522-0.2020.0570.07390.072500.9087-0.0454-0.04790.9424-0.11170.631162.907553.553765.673
40.5518-0.4443-0.23560.53970.00640.3805-0.00050.18290.0546-0.2393-0.0203-0.23290.26680.0753-00.68510.00630.08430.65350.03110.736296.405149.690677.1488
5-0.4158-1.66-0.84681.69990.55580.2970.02520.0528-0.05420.0291-0.01910.0162-0.0347-0.13370.00480.4637-0.00860.02850.44020.01790.406773.606465.938994.5479
61.2792-0.20810.10351.18110.43180.089-0.22010.18060.04880.3690.07950.2735-0.0451-0.170500.91390.19280.03610.72930.0030.828850.857891.1247104.6933
70.64580.31450.25910.218-0.16190.5469-0.17470.05170.1082-0.08640.07310.0082-0.00470.012700.7342-0.1583-0.00950.7412-0.11950.680144.685343.062286.6453
80.41460.28340.63331.04590.26740.21770.0028-0.32270.00660.0606-0.0222-0.07150.0205-0.1168-00.6358-0.05960.06860.68520.02190.594168.285744.5973123.92
9-0.01170.01550.00240.0925-0.00430.05660.38810.0253-0.1898-0.23930.1372-0.4861-0.22630.8409-0.00020.8883-0.104-0.02370.9062-0.10310.763587.954453.4634124.8749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:178)
2X-RAY DIFFRACTION2(chain A and resid 179:336)
3X-RAY DIFFRACTION3(chain A and resid 337:493)
4X-RAY DIFFRACTION4(chain B and resid 6:106)
5X-RAY DIFFRACTION5(chain B and resid 107:336)
6X-RAY DIFFRACTION6(chain B and resid 337:492)
7X-RAY DIFFRACTION7(chain C and resid 6:336)
8X-RAY DIFFRACTION8(chain C and resid 337:474)
9X-RAY DIFFRACTION9(chain C and resid 475:493)

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