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- PDB-4u1e: Crystal structure of the eIF3b-CTD/eIF3i/eIF3g-NTD translation in... -

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Basic information

Entry
Database: PDB / ID: 4u1e
TitleCrystal structure of the eIF3b-CTD/eIF3i/eIF3g-NTD translation initiation complex
Components
  • Eukaryotic translation initiation factor 3 subunit BEukaryotic initiation factor 3
  • Eukaryotic translation initiation factor 3 subunit GEukaryotic initiation factor 3
  • Eukaryotic translation initiation factor 3 subunit IEukaryotic initiation factor 3
KeywordsTRANSLATION / translation initiation / eIF3 complex / beta-propeller
Function / homology
Function and homology information


: / translation reinitiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation ...: / translation reinitiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / 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 termination / translation initiation factor binding / translational initiation / translation initiation factor activity / cytoplasmic stress granule / RNA binding / identical protein binding
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / 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 ...Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / 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 / WD40 repeat, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit G
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsZhang, S. / Erzberger, J.P. / Schaefer, T. / Ban, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council250071 Switzerland
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
I: Eukaryotic translation initiation factor 3 subunit I
B: Eukaryotic translation initiation factor 3 subunit B
G: Eukaryotic translation initiation factor 3 subunit G


Theoretical massNumber of molelcules
Total (without water)60,0123
Polymers60,0123
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-29 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.270, 130.290, 192.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsbiological unit is the same as asym.

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit I / Eukaryotic initiation factor 3 / eIF3i / Eukaryotic translation initiation factor 3 39 kDa subunit homolog / eIF-3 39 kDa subunit homolog


Mass: 38803.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: TIF34, SCY_4321 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pRIL / References: UniProt: A6ZMK5
#2: Protein/peptide Eukaryotic translation initiation factor 3 subunit B / Eukaryotic initiation factor 3 / 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


Mass: 5677.446 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: PRT1, CDC63, YOR361C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06103
#3: Protein Eukaryotic translation initiation factor 3 subunit G / Eukaryotic initiation factor 3 / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Translation initiation factor eIF3 p33 subunit / eIF3 p33


Mass: 15530.686 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: TIF35, YDR429C, D9461.16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04067
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: PEG 20000, PEG MME 550, imidazole, MES / PH range: 6.3-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2→50 Å / Num. obs: 46648 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.25
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-IDRejects% possible all
2-2.111.941099.8
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.3_1479)refinement
RefinementResolution: 2→48.49 Å / FOM work R set: 0.7615 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2397 5.14 %Random selection
Rwork0.1858 44226 --
obs0.1874 46623 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.58 Å2 / Biso mean: 54.11 Å2 / Biso min: 30.26 Å2
Refinement stepCycle: final / Resolution: 2→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3719 0 0 203 3922
Biso mean---53.35 -
Num. residues----466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063798
X-RAY DIFFRACTIONf_angle_d0.9545121
X-RAY DIFFRACTIONf_chiral_restr0.039554
X-RAY DIFFRACTIONf_plane_restr0.004654
X-RAY DIFFRACTIONf_dihedral_angle_d11.8721407
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.04080.38611390.355325612700
2.0408-2.08520.34071390.327525772716
2.0852-2.13370.33021370.297525512688
2.1337-2.18710.28891380.266625642702
2.1871-2.24620.33711400.257625672707
2.2462-2.31230.28151390.241725702709
2.3123-2.3870.26791410.227625872728
2.387-2.47230.23991400.21625902730
2.4723-2.57120.23271390.205125712710
2.5712-2.68830.25021420.199925942736
2.6883-2.830.23341410.201325962737
2.83-3.00730.24811400.195225972737
3.0073-3.23940.2381410.194926042745
3.2394-3.56530.20981430.168426152758
3.5653-4.0810.19741430.157626472790
4.081-5.14070.15131430.137226512794
5.1407-48.50370.18691520.177627842936
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)
10.56240.63790.25440.43940.31521.02440.06030.3450.0517-0.04570.0387-0.0112-0.13380.40460.00010.40580.02130.02180.47380.03930.37945.1477-23.291710.5831
20.9016-0.3054-0.04460.73730.32490.2034-0.04820.1672-0.0558-0.1290.06110.1717-0.0248-0.3014-00.41240.0385-0.01850.44160.0110.4008-11.7829-25.809214.6299
30.5561-0.43830.03180.6186-0.43620.90380.1064-0.09530.00630.0517-0.10190.13370.0557-0.399200.36290.0428-0.01120.48520.01180.4427-14.8879-28.035627.6495
40.3378-0.02910.380.3101-0.22120.59150.0248-0.16550.0125-0.08990.06150.06410.0098-0.063500.32710.01560.00150.3715-0.02650.3851-0.7483-20.773735.1443
50.8032-0.02730.34410.183-0.05450.62420.05560.07250.1364-0.0703-0.1221-0.0254-0.150.4175-0.00010.4046-0.00690.00050.49440.01240.429910.4847-18.417426.8402
60.5305-0.2614-0.25630.3534-0.0190.85860.06930.2250.0855-0.1688-0.1756-0.14940.19970.9719-0.02690.38730.09520.01040.57930.01780.400618.5117-26.997928.9243
71.1031-0.5157-0.56090.82890.21292.2850.17950.00250.0930.27280.0238-0.00690.02620.44880.01650.44760.03470.00390.49780.06270.399811.3898-28.946946.4701
80.1019-0.0867-0.05310.0690.00120.03660.2628-0.45310.1394-0.1268-0.2214-0.06850.36380.1140.0010.50780.0396-0.04840.41720.00070.58733.4964-40.557630.9411
90.5874-0.3031-0.26970.3523-0.03670.17620.29160.21790.27990.68-0.4713-0.07430.11730.3321-0.00090.82440.0136-0.16450.71150.19530.61520.5085-68.55696.588
100.0911-0.13030.06820.1942-0.20280.21250.07520.176-0.0635-0.2094-0.09920.1635-0.03930.2102-0.00030.67240.0404-0.01280.48470.09710.386118.5361-73.3932-1.458
110.02920.04190.01850.0786-0.01070.0870.0789-0.5550.28560.11260.3298-0.2575-0.454-0.0048-0.00030.84520.02220.09380.68840.02940.548619.3171-46.15297.8105
120.0548-0.05960.04610.0919-0.01480.0672-0.2157-0.29980.0846-0.2403-0.08280.21860.2904-0.0638-0.00140.74030.08410.05680.4148-0.08370.59996.86-40.79677.364
130.21720.0156-0.17340.02630.01970.09150.01790.84090.15950.2247-0.08680.17010.1238-0.2515-0.00030.49070.02550.01230.5395-0.05520.43914.1163-29.8387-1.7122
140.03040.0427-0.03090.0473-0.04080.0231-0.0016-0.08630.28240.3079-0.05940.00790.06771.1581-0.00010.47090.0717-0.00840.70820.06080.416415.3815-21.84442.9606
150.28790.15290.06080.02330.03680.03930.33310.00320.4445-0.01350.6984-0.283-0.2060.22090.0020.518-0.08920.05410.7173-0.05770.601722.7709-17.861326.8338
160.0484-0.06110.02850.0717-0.03380.0115-0.48880.40070.03880.1135-0.12971.1027-0.8164-0.2553-0.00311.385-0.0262-0.27420.8213-0.13870.889424.6699-8.153631.6811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 48 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 49 through 129 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 130 through 192 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 193 through 235 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 236 through 312 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 313 through 342 )B0
7X-RAY DIFFRACTION7chain 'E' and (resid 652 through 689 )E0
8X-RAY DIFFRACTION8chain 'E' and (resid 690 through 698 )E0
9X-RAY DIFFRACTION9chain 'A' and (resid 8 through 25 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 26 through 36 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 37 through 46 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 47 through 54 )A0
13X-RAY DIFFRACTION13chain 'A' and (resid 55 through 66 )A0
14X-RAY DIFFRACTION14chain 'A' and (resid 67 through 76 )A0
15X-RAY DIFFRACTION15chain 'A' and (resid 77 through 86 )A0
16X-RAY DIFFRACTION16chain 'A' and (resid 87 through 96 )A0

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