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- PDB-3ns6: Crystal structure of hte RNA recognition motif of yeast eIF3b res... -

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Basic information

Entry
Database: PDB / ID: 3ns6
TitleCrystal structure of hte RNA recognition motif of yeast eIF3b residues 76-170
ComponentsEukaryotic translation initiation factor 3 subunit B
KeywordsTRANSLATION
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / cytoplasmic translational initiation / multi-eIF complex / 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 / cytoplasmic translational initiation / multi-eIF complex / 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 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKhoshnevis, S. / Neumann, P. / Ficner, R.
CitationJournal: Plos One / Year: 2010
Title: Crystal structure of the RNA recognition motif of yeast translation initiation factor eIF3b reveals differences to human eIF3b.
Authors: Khoshnevis, S. / Neumann, P. / Ficner, R.
History
DepositionJul 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5446
Polymers22,1602
Non-polymers3844
Water5,423301
1
A: Eukaryotic translation initiation factor 3 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2723
Polymers11,0801
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 3 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2723
Polymers11,0801
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.713, 51.752, 77.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Eukaryotic translation initiation factor 3 90 kDa subunit / eIF3 p90 / Translation ...eIF3b / Eukaryotic translation initiation factor 3 90 kDa subunit / eIF3 p90 / Translation initiation factor eIF3 p90 subunit / Cell cycle regulation and translation initiation protein


Mass: 11079.933 Da / Num. of mol.: 2 / Fragment: residues 76-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC63, PRT1, YOR361C / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P06103
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG4000, 200 mM Li2SO4 and 100 mM Hepes pH 8. The crystals were grown in a sitting drop at 20 degrees by mixing 1uL of protein (11 mg/mL) with 1uL of reservoir, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.25→38.026 Å / Num. obs: 48971 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.437 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.25-1.330.5034.241259816999.4
1.33-1.390.375.6260614965100
1.39-1.470.2777.128957546099.9
1.47-1.550.1989.223573440199.9
1.55-2.080.10114.2804191506399.8
2.08-2.660.06420.929234559599.4
2.66-3.240.05623.311875232298.9
3.24-3.820.04826.95735113499
3.82-4.40.04427314862697.8
4.4-100.0428.45377111798.2
10-200.03222.336110191.8
20-300.04319.7441392.9
300.03819.514555.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SXL

3sxl


Resolution: 1.25→38.026 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.9161 / SU ML: 0.11 / σ(F): 1.36 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1675 2442 4.99 %
Rwork0.1416 --
obs0.1429 48895 99.55 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.565 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 42.61 Å2 / Biso mean: 13.5729 Å2 / Biso min: 4.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.1087 Å2-0 Å20 Å2
2---1.8208 Å20 Å2
3---1.5959 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 20 301 1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011707
X-RAY DIFFRACTIONf_angle_d1.3262310
X-RAY DIFFRACTIONf_chiral_restr0.091252
X-RAY DIFFRACTIONf_plane_restr0.008293
X-RAY DIFFRACTIONf_dihedral_angle_d10.658659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.27550.22381400.16822655279599
1.2755-1.30330.2211420.16962700284299
1.3033-1.33360.21691420.161827022844100
1.3336-1.36690.18941430.145927112854100
1.3669-1.40390.19751430.139427292872100
1.4039-1.44520.17571410.133126842825100
1.4452-1.49190.16451420.125326972839100
1.4919-1.54520.16421440.121727242868100
1.5452-1.6070.16661430.115627412884100
1.607-1.68020.16211430.120427252868100
1.6802-1.76880.17351430.125827302873100
1.7688-1.87960.14311430.128727332876100
1.8796-2.02470.17781440.124727312875100
2.0247-2.22840.14511450.125627522897100
2.2284-2.55080.16171470.15072776292399
2.5508-3.21350.17611450.15842785293099
3.2135-38.04340.1491520.15012878303098

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