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- PDB-3ns5: Crystal structure of the RNA recognition motif of yeast eIF3b res... -

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Basic information

Entry
Database: PDB / ID: 3ns5
TitleCrystal structure of the RNA recognition motif of yeast eIF3b residues 76-161
ComponentsEukaryotic translation initiation factor 3 subunit B
KeywordsTRANSLATION
Function / homology
Function and homology information


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 ...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 / 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 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 / MOLECULAR REPLACEMENT / Resolution: 2.598 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)19,9702
Polymers19,9702
Non-polymers00
Water90150
1
A: Eukaryotic translation initiation factor 3 subunit B


Theoretical massNumber of molelcules
Total (without water)9,9851
Polymers9,9851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 3 subunit B


Theoretical massNumber of molelcules
Total (without water)9,9851
Polymers9,9851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.280, 68.140, 81.890
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: 9984.877 Da / Num. of mol.: 2 / Fragment: residues 76-161
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: 33% PEG4000 and 0.1 M Na-citrate (pH 5.6) in a sitting drop plate at 20 degrees. 1uL of protein at the concentration of 17 mg/mL was mixed with 1 uL of reservoir, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5417 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.598→34.16 Å / Num. all: 5632 / Num. obs: 5632 / % possible obs: 99.1 % / Redundancy: 4.4 % / Rsym value: 0.111 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.59-2.734.20.322.432767710.3294.6
2.73-2.94.50.2952.633317410.29599.9
2.9-3.14.50.2193.532877290.21999.9
3.1-3.354.60.1475.130786740.147100
3.35-3.674.50.116.927816180.11100
3.67-4.14.50.089.325645720.08100
4.1-4.734.50.05612.822615030.056100
4.73-5.84.40.0641119594500.064100
5.8-8.24.20.05812.614873580.058100
8.2-34.073.70.03119.77952160.03198.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NS6

3ns6


Resolution: 2.598→31.456 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7899 / SU ML: 0.62 / σ(F): 0.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2725 279 5 %
Rwork0.225 --
obs0.2274 5584 99.38 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.136 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 123.21 Å2 / Biso mean: 24.461 Å2 / Biso min: 3.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.6301 Å20 Å2-0 Å2
2--3.8699 Å2-0 Å2
3----3.2398 Å2
Refinement stepCycle: LAST / Resolution: 2.598→31.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 0 50 1442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011420
X-RAY DIFFRACTIONf_angle_d0.481902
X-RAY DIFFRACTIONf_chiral_restr0.033218
X-RAY DIFFRACTIONf_plane_restr0.002232
X-RAY DIFFRACTIONf_dihedral_angle_d9.774540
LS refinement shellResolution: 2.5981→3.2728 Å / Total num. of bins used: 2
RfactorNum. reflection% reflection
Rfree0.3635 138 -
Rwork0.2796 2574 -
all-2712 -
obs--99 %
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)
10.405-0.65050.00881.0064-0.04640.3751-0.1612-0.0067-0.03590.20520.14430.03080.0427-0.06350.0910.0813-0.00940.00550.072-0.04550.04564.66782.382717.7549
20.4965-0.0954-0.00130.4492-0.19660.2057-0.09090.0838-0.0207-0.1474-0.0065-0.04110.03290.094-0.0470.05140.0462-0.01380.0072-0.0260.08080.88471.1908-2.8641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA72
2X-RAY DIFFRACTION2chain BB72 - 1

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