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- PDB-1ijf: Nucleotide exchange mechanisms in the eEF1A-eEF1Ba complex -

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Basic information

Entry
Database: PDB / ID: 1ijf
TitleNucleotide exchange mechanisms in the eEF1A-eEF1Ba complex
Components
  • elongation factor 1-alpha
  • elongation factor 1-beta
KeywordsTRANSLATION / protein complex
Function / homology
Function and homology information


Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / HSF1 activation / melatonin binding / regulation of translational termination / tRNA export from nucleus / Protein methylation / fungal-type vacuole membrane / translational elongation ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / HSF1 activation / melatonin binding / regulation of translational termination / tRNA export from nucleus / Protein methylation / fungal-type vacuole membrane / translational elongation / actin filament bundle assembly / translation elongation factor activity / Neutrophil degranulation / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / negative regulation of protein phosphorylation / maintenance of translational fidelity / negative regulation of protein kinase activity / GDP binding / actin filament binding / ribosome binding / cytoskeleton / ribosome / translation / GTPase activity / GTP binding / protein kinase binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / : / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain ...Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / : / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain / EF-1 guanine nucleotide exchange domain / Translation elongation factor EF1A, eukaryotic/archaeal / Ribosomal protein S6/Translation elongation factor EF1B / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Glutathione S-transferase, C-terminal domain superfamily / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation elongation factor EF1B/ribosomal protein S6 / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor 1-alpha / Elongation factor 1-beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAndersen, G.R. / Valente, L. / Pedersen, L. / Kinzy, T.G. / Nyborg, J.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex.
Authors: Andersen, G.R. / Valente, L. / Pedersen, L. / Kinzy, T.G. / Nyborg, J.
#1: Journal: Mol.Cell / Year: 2000
Title: Structural Basis for Nucleotide Exchange and Competition with tRNA in the Yeast Elongation Factor Complex eEF1A:eEF1Balpha
Authors: Andersen, G.R. / Pedersen, L. / Valente, L. / Chatterjee, I.I. / Kinzy, T.G. / Kjeldgaard, M. / Nyborg, J.
History
DepositionApr 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: elongation factor 1-alpha
B: elongation factor 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6244
Polymers60,1572
Non-polymers4682
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-22 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.247, 91.728, 92.713
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 elongation factor 1-alpha / eEF1A


Mass: 50110.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02994
#2: Protein elongation factor 1-beta / eEF1Ba


Mass: 10046.277 Da / Num. of mol.: 1 / Fragment: catalytical C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TEF5 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): 834 DE3 / References: UniProt: P32471
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: mmE2K, Tris, Hepes, KCl, DTT, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.2
Details: Pedersen, L.P., (2000) Acta Crystallogr., D57, 159.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMHEPES1drop
3100 mM1dropKCl
40.5 mMdithiothreitol1drop
5100 mM1reservoirKCl
6100 mMTris-HCl1reservoir
73 mMdithiothreitol1reservoir
815-18 %PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 13, 2000
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→14 Å / Num. all: 11251 / Num. obs: 10905 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.172 / % possible all: 91
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 14 Å
Reflection shell
*PLUS
% possible obs: 91 % / Mean I/σ(I) obs: 5.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1f60

1f60


Resolution: 3→13.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 133306.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 573 5.3 %RANDOM
Rwork0.25 ---
all0.251 11916 --
obs0.25 10866 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-14.06 Å20 Å20 Å2
2---1.98 Å20 Å2
3----12.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3→13.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 25 0 4116
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d2.01
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 87 5.6 %
Rwork0.335 1457 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PArAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION35GP_PAR5005GP_TOP
X-RAY DIFFRACTION4MG135.PARamMG_XPLOR_TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5.3 % / Rfactor obs: 0.25 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.01
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.388 / % reflection Rfree: 5.6 % / Rfactor Rwork: 0.335

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