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- PDB-4k51: Crystal Structure of the PCI domain of eIF3a -

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Basic information

Entry
Database: PDB / ID: 4k51
TitleCrystal Structure of the PCI domain of eIF3a
ComponentsEukaryotic translation initiation factor 3 subunit A
KeywordsBIOSYNTHETIC PROTEIN / eIF3 / PCI domain / translation initiation
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
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #860 / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsKhoshnevis, S. / Neumann, P. / Ficner, R.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes.
Authors: Khoshnevis, S. / Gunisova, S. / Vlckova, V. / Kouba, T. / Neumann, P. / Beznoskova, P. / Ficner, R. / Valasek, L.S.
History
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 A
B: Eukaryotic translation initiation factor 3 subunit A


Theoretical massNumber of molelcules
Total (without water)51,2282
Polymers51,2282
Non-polymers00
Water00
1
A: Eukaryotic translation initiation factor 3 subunit A


Theoretical massNumber of molelcules
Total (without water)25,6141
Polymers25,6141
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)25,6141
Polymers25,6141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.140, 137.140, 137.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit A / 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: 25614.117 Da / Num. of mol.: 2 / Fragment: PCI, UNP residues 276-494
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 (E. coli) / References: UniProt: P38249

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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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG, buffer, salt, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 46241

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.65→48.486 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2861 630 5.01 %
Rwork0.2489 --
obs0.2508 12582 99.53 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→48.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 0 0 3032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063100
X-RAY DIFFRACTIONf_angle_d1.2654207
X-RAY DIFFRACTIONf_dihedral_angle_d15.3571141
X-RAY DIFFRACTIONf_chiral_restr0.074493
X-RAY DIFFRACTIONf_plane_restr0.006520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.85470.2961250.32312370X-RAY DIFFRACTION100
2.8547-3.14190.4271250.31172378X-RAY DIFFRACTION100
3.1419-3.59640.29951250.26492359X-RAY DIFFRACTION100
3.5964-4.53060.25661260.22752393X-RAY DIFFRACTION99
4.5306-48.49440.26851290.23122452X-RAY DIFFRACTION99
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)
12.00780.4094-0.64121.61630.1641.3861-0.0003-0.03170.33530.23120.02550.1406-0.28870.2297-0.01610.423-0.03430.00440.2449-0.01010.265767.82219.90496.5898
20.576-0.03010.01380.3011-0.67220.0239-0.01920.1532-0.1755-0.0525-0.1390.22280.29520.382-0.08750.5590.00350.04880.26070.05220.284470.835-0.416520.1335
30.00580.07130.03650.0183-0.0054-0.0047-0.2250.3202-0.2192-0.78850.1603-0.35910.1565-0.63450.00031.58160.1902-0.05131.48-0.19341.1965-39.5825-36.558316.1949
4-0.0309-0.06210.0434-0.00230.0499-0.0052-0.10550.7243-0.1121-0.19790.62590.09610.31190.3073-0.00021.60980.3285-0.08631.3171-0.0811.0625-33.5944-33.325710.6441
5-0.0138-0.1448-0.0524-0.0989-0.0484-0.0226-0.3717-0.17620.1902-0.14720.23010.1306-0.07690.2392-0.00011.64580.59310.24871.54930.24391.438-33.1386-23.635310.6111
6-0.0148-0.0607-0.01250.02060.07510.0492-0.3070.56510.4391-0.33270.2437-0.40440.2411-0.43060.00021.05820.14770.2141.8560.67071.62-16.8561-25.525615.6953
7-0.01450.00030.0521-0.04970.0245-0.0259-0.56510.1163-0.01030.1248-0.9168-0.26490.0412-0.115200.9882-0.17590.10451.56910.23251.5813-19.5098-19.332724.7058
80.0006-0.06240.04150.0650.2002-0.0639-0.1350.05410.35920.78320.0016-0.2790.5770.18-0.00131.00980.30190.35131.46240.3441.2853-14.6714-34.374929.5667
9-0.0496-0.0583-0.02730.0193-0.07050.04430.03830.82460.35050.85220.4822-0.57640.12530.4443-0.00020.78640.0967-0.33771.4662-0.15711.8773-15.8502-32.561237.3806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 278 through 417 )
2X-RAY DIFFRACTION2chain 'A' and (resid 418 through 493 )
3X-RAY DIFFRACTION3chain 'B' and (resid 278 through 295 )
4X-RAY DIFFRACTION4chain 'B' and (resid 296 through 312 )
5X-RAY DIFFRACTION5chain 'B' and (resid 313 through 333 )
6X-RAY DIFFRACTION6chain 'B' and (resid 334 through 399 )
7X-RAY DIFFRACTION7chain 'B' and (resid 400 through 417 )
8X-RAY DIFFRACTION8chain 'B' and (resid 418 through 444 )
9X-RAY DIFFRACTION9chain 'B' and (resid 445 through 475 )

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