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- PDB-4u1f: Crystal structure of middle domain of eukaryotic translation init... -

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Basic information

Entry
Database: PDB / ID: 4u1f
TitleCrystal structure of middle domain of eukaryotic translation initiation factor eIF3b
ComponentsEukaryotic translation initiation factor 3 subunit B
KeywordsTRANSLATION / translation initiation / eIF3 complex / beta-propeller
Function / homology
Function and homology information


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 ...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
Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,8722
Polymers113,8722
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-42 kcal/mol
Surface area45980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.160, 175.870, 71.320
Angle α, β, γ (deg.)90.000, 113.620, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein 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


Mass: 56935.961 Da / Num. of mol.: 2
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 (E. coli) / References: UniProt: P06103
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: PEG MME 5000, potassium thiocyanate, CHES / PH range: 8-9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00, 0.9793
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
ReflectionResolution: 2.2→50 Å / Num. obs: 67154 / % possible obs: 97.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 18.51
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 1.83 / % possible all: 97.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
XSCALEdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→43.637 Å / FOM work R set: 0.8066 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 4040 6.02 %Random selection
Rwork0.1871 63094 --
obs0.1895 67134 97.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.12 Å2 / Biso mean: 55.3 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 2.2→43.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7685 0 0 207 7892
Biso mean---48.27 -
Num. residues----949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077909
X-RAY DIFFRACTIONf_angle_d1.01110756
X-RAY DIFFRACTIONf_chiral_restr0.071143
X-RAY DIFFRACTIONf_plane_restr0.0041388
X-RAY DIFFRACTIONf_dihedral_angle_d12.3972874
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1999-2.22580.33281330.31622093222695
2.2258-2.2530.31511400.28362146228697
2.253-2.28150.32741230.28422197232098
2.2815-2.31150.31131500.2632212236299
2.3115-2.34320.32621380.25712184232299
2.3432-2.37660.3191280.25792166229498
2.3766-2.41210.27961470.24582221236899
2.4121-2.44980.29211410.24262156229799
2.4498-2.490.33121470.23242188233599
2.49-2.53290.31111420.24442175231799
2.5329-2.57890.25351300.24142195232598
2.5789-2.62850.28441420.23842213235599
2.6285-2.68220.31321400.23812181232199
2.6822-2.74050.29821410.22812194233597
2.7405-2.80420.28141410.21652147228898
2.8042-2.87440.2611440.21252180232498
2.8744-2.95210.25691390.21492177231698
2.9521-3.03890.26761380.212178231698
3.0389-3.1370.23881430.21322189233299
3.137-3.2490.26141280.20762206233499
3.249-3.37910.24131470.19782200234799
3.3791-3.53280.2351400.18342154229496
3.5328-3.7190.21051340.18312120225496
3.719-3.95180.23181400.17482205234599
3.9518-4.25670.17181430.14872185232898
4.2567-4.68460.16331420.12932192233498
4.6846-5.36150.17161380.14322091222994
5.3615-6.75090.18891490.17562165231497
6.7509-43.64520.22181320.18052184231696
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)
13.18270.7023-0.63373.13820.52332.9416-0.10880.62370.0613-0.6772-0.02830.5328-0.0877-0.33780.1380.42150.0263-0.04280.4269-0.0020.355225.8643102.800214.1527
21.5456-0.3509-0.90591.28560.40431.4845-0.0560.67830.0218-0.4315-0.0073-0.34750.28170.17050.06730.6736-0.0340.17780.64030.07170.350944.9234102.83044.634
31.74850.31330.14111.220.82753.1882-0.00520.27890.1492-0.3815-0.0634-0.5323-0.080.43110.07090.4701-0.02270.17550.45060.09040.492453.248111.99618.4841
43.15320.4179-0.19271.48480.90952.52980.1923-0.3010.24930.0909-0.1528-0.59810.04750.5212-0.01330.3497-0.0590.03990.47710.07210.602355.2566111.825536.1857
52.33390.83520.0752.1887-0.54192.10040.2046-0.4133-0.04730.461-0.3401-0.3680.00290.29890.03460.3941-0.0477-0.00780.40440.04950.348143.9079106.233545.5079
62.54290.60480.37541.7424-0.22182.32550.1538-0.6113-0.14910.4828-0.21060.24970.0748-0.08760.11210.3681-0.0360.08890.39870.04460.316431.306101.915244.4692
70.5831.04410.40193.93660.23341.43170.0768-0.059-0.3146-0.2364-0.0210.30680.3224-0.1331-0.11490.34240.00050.08380.23640.02670.379129.405993.761430.3186
81.26460.0548-0.04832.56490.24010.9354-0.10720.17640.2123-0.7892-0.0625-0.858-0.23230.28360.01960.2902-0.0113-0.03950.26410.05320.452437.446461.406926.9002
92.80311.1260.31423.36640.06281.9939-0.21120.62120.0726-1.2060.07930.1642-0.0173-0.21970.12650.78650.0083-0.11410.4757-0.03170.239322.774455.125111.6695
102.28610.7533-0.50283.3133-0.12192.260.0764-0.24150.02470.2342-0.28580.5337-0.0377-0.36880.1050.2518-0.014-0.02720.3165-0.09380.361617.089752.671338.35
111.1415-0.1566-0.2482.7145-0.28031.3657-0.14070.1434-0.2515-0.5345-0.08690.53670.2151-0.44570.24760.19680.00070.04960.29960.00320.386323.992298.185526.3848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 146 through 212 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 272 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 354 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 355 through 433 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 434 through 505 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 506 through 564 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 565 through 596 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 597 through 625 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 315 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 316 through 596 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 597 through 625 )B0

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