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- PDB-2iu1: Crystal structure of eIF5 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2iu1
TitleCrystal structure of eIF5 C-terminal domain
ComponentsEUKARYOTIC TRANSLATION INITIATION FACTOR 5
KeywordsTRANSCRIPTION / MFC / EIF5 / GTP-BINDING / PHOSPHORYLATION / PROTEIN BIOSYNTHESIS / TRANSLATION INITITATION / INITIATION FACTOR / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


eukaryotic initiation factor eIF2 binding / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / GDP-dissociation inhibitor activity / regulation of translational initiation / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor activity / ribosome assembly / GTPase activator activity ...eukaryotic initiation factor eIF2 binding / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / GDP-dissociation inhibitor activity / regulation of translational initiation / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor activity / ribosome assembly / GTPase activator activity / cadherin binding / synapse / GTP binding / RNA binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsBieniossek, C. / Schuetz, P. / Baumann, U.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of the Carboxy-Terminal Domain of Human Translation Initiation Factor Eif5.
Authors: Bieniossek, C. / Schutz, P. / Bumann, M. / Limacher, A. / Uson, I. / Baumann, U.
History
DepositionMay 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_residues / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 5


Theoretical massNumber of molelcules
Total (without water)24,4431
Polymers24,4431
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.137, 70.254, 81.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 5 / EIF5


Mass: 24442.861 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN RESIDUES 232-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55010
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 0.2 M MGCL2, 0.1 M TRIS PH 8.5, 25% PEG 3350, 20 DEG C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.008
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 104040 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.6
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 8.5 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.783 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DISORDERED AA-BOX2 RESIDUES 385 - 397 WERE MODELED BY MODELLER FISER AND SALI, PROT SCI 9, P1753- 1773, 2000. OCCUPANCIES SET TO 0.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1287 7.3 %RANDOM
Rwork0.185 ---
obs0.188 16243 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 0 139 1612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221390
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.181.9791860
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4075162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00424.54566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44915297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.588159
X-RAY DIFFRACTIONr_chiral_restr0.090.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02997
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.2694
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.2977
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1753.5835
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53931328
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3094610
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7055.5532
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 88
Rwork0.202 1171
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)
19.9974-4.9181-3.71644.59453.15144.13150.1450.3703-0.1056-0.3325-0.19180.1007-0.0654-0.2250.0468-0.0891-0.0408-0.0177-0.13160.0267-0.169311.157554.58685.8464
21.30880.35270.00362.7709-1.53391.5648-0.037-0.0974-0.10450.00260.01460.05520.0796-0.00990.0224-0.14180.00620.0032-0.1312-0.0153-0.136116.130847.385520.0601
34.0718-2.11581.85712.4485-2.24342.4443-0.1148-0.16610.03080.21490.0784-0.0011-0.0945-0.05710.0365-0.0651-0.02680.0294-0.096-0.0407-0.0727.068345.475827.0214
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A232 - 259
2X-RAY DIFFRACTION2A260 - 360
3X-RAY DIFFRACTION3A361 - 409

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