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- PDB-9f79: Crystal structure of the S. cerevisiae eIF2beta N-terminal tail b... -

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Basic information

Entry
Database: PDB / ID: 9f79
TitleCrystal structure of the S. cerevisiae eIF2beta N-terminal tail bound to the C-terminal domain of eIF5
Components
  • Eukaryotic translation initiation factor 2 subunit beta
  • Eukaryotic translation initiation factor 5
KeywordsTRANSLATION / Eukaryotic translation initiation factor / Complex / eIF5 / W2 domain / eIF2 beta
Function / homology
Function and homology information


eukaryotic initiation factor eIF2 binding / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex ...eukaryotic initiation factor eIF2 binding / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / GDP-dissociation inhibitor activity / 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 / negative regulation of translational initiation / GTPase activator activity / cytosolic ribosome assembly / translational initiation / ribosome / mRNA binding / GTP binding / zinc ion binding / cytosol
Similarity search - Function
Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Armadillo-type fold
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2 subunit beta / Eukaryotic translation initiation factor 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKuhle, B. / Marintchev, A. / Ficner, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rna / Year: 2025
Title: Molecular basis for the interactions of eIF2 beta with eIF5, eIF2B, and 5MP1 and their regulation by CK2.
Authors: Wagner, P.A. / Song, M. / Doran, P. / Seker, A. / Ficner, R. / Kuhle, B. / Marintchev, A.
History
DepositionMay 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5
B: Eukaryotic translation initiation factor 5
C: Eukaryotic translation initiation factor 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)55,5513
Polymers55,5513
Non-polymers00
Water4,053225
1
A: Eukaryotic translation initiation factor 5
C: Eukaryotic translation initiation factor 2 subunit beta

A: Eukaryotic translation initiation factor 5
C: Eukaryotic translation initiation factor 2 subunit beta

B: Eukaryotic translation initiation factor 5

B: Eukaryotic translation initiation factor 5


Theoretical massNumber of molelcules
Total (without water)111,1036
Polymers111,1036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area15400 Å2
ΔGint-97 kcal/mol
Surface area43250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.180, 74.180, 224.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

21A-557-

HOH

31B-565-

HOH

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Components

#1: Protein Eukaryotic translation initiation factor 5 / eIF-5


Mass: 23934.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIF5, YPR041W, YP3085.05 / Production host: Escherichia coli (E. coli) / References: UniProt: P38431
#2: Protein Eukaryotic translation initiation factor 2 subunit beta / eIF2-beta


Mass: 7681.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUI3, TIF212, YPL237W / Production host: Escherichia coli (E. coli) / References: UniProt: P09064
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.4 M (NH4)2SO4, 0.08 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 359597 / % possible obs: 99.9 % / Redundancy: 7.45 % / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.064 / Net I/σ(I): 22.34
Reflection shellResolution: 2→2.2 Å / Rmerge(I) obs: 0.428 / Num. unique obs: 11831 / Rrim(I) all: 0.537 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.4 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2277 2411 5 %
Rwork0.2067 --
obs0.2077 48210 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 0 225 3781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015
X-RAY DIFFRACTIONf_angle_d1.645
X-RAY DIFFRACTIONf_dihedral_angle_d5.705483
X-RAY DIFFRACTIONf_chiral_restr0.173556
X-RAY DIFFRACTIONf_plane_restr0.012647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.27651380.27462632X-RAY DIFFRACTION99
2.04-2.090.29121400.25842664X-RAY DIFFRACTION100
2.09-2.130.30761410.23642673X-RAY DIFFRACTION100
2.13-2.190.24391420.23332696X-RAY DIFFRACTION100
2.19-2.250.25171400.21752658X-RAY DIFFRACTION100
2.25-2.310.25531410.21952685X-RAY DIFFRACTION100
2.31-2.390.251410.23032674X-RAY DIFFRACTION100
2.39-2.470.23041410.2262681X-RAY DIFFRACTION100
2.47-2.570.28051410.22592674X-RAY DIFFRACTION100
2.57-2.690.26071410.222677X-RAY DIFFRACTION100
2.69-2.830.24251410.21372681X-RAY DIFFRACTION100
2.83-3.010.23121420.21752692X-RAY DIFFRACTION100
3.01-3.240.22811430.22412713X-RAY DIFFRACTION100
3.24-3.560.23191420.20012706X-RAY DIFFRACTION100
3.56-4.080.20981430.192721X-RAY DIFFRACTION100
4.08-5.140.19971450.17352742X-RAY DIFFRACTION100
5.14-37.40.18621490.19072830X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.7106 Å / Origin y: 9.4274 Å / Origin z: 18.1643 Å
111213212223313233
T0.355 Å20.1137 Å2-0.0043 Å2-0.2425 Å20.0332 Å2--0.1937 Å2
L0.6094 °2-0.2534 °20.006 °2-0.8854 °20.0537 °2--0.9034 °2
S0.0664 Å °-0.2121 Å °-0.0376 Å °0.1621 Å °0.0342 Å °0.0219 Å °0.0012 Å °0.1011 Å °-0.0741 Å °
Refinement TLS groupSelection details: all

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