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- PDB-5xln: Crystal structure of the TRS_UNE-T and 4EHP complex -

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Basic information

Entry
Database: PDB / ID: 5xln
TitleCrystal structure of the TRS_UNE-T and 4EHP complex
Components
  • Eukaryotic translation initiation factor 4E type 2
  • Threonine--tRNA ligase, cytoplasmic
KeywordsRNA BINDING PROTEIN/LIGASE / TRS / 4EHP / Complex / RNA BINDING PROTEIN-LIGASE complex
Function / homology
Function and homology information


threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / RNA cap binding / eukaryotic translation initiation factor 4F complex / Cytosolic tRNA aminoacylation / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding ...threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / RNA cap binding / eukaryotic translation initiation factor 4F complex / Cytosolic tRNA aminoacylation / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / rescue of stalled ribosome / negative regulation of translational initiation / translation initiation factor activity / P-body / ISG15 antiviral mechanism / tRNA binding / negative regulation of translation / ubiquitin protein ligase binding / RNA binding / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Beta-grasp domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E type 2 / Threonine--tRNA ligase 1, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsHwang, J. / Nguyen, L.T. / Kim, M.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of Science, ICT & Future Planning of KoreaNRF-2010-0029767 Korea, Republic Of
KRIBB Initiative ProgramKGM4541622 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2019
Title: A threonyl-tRNA synthetase-mediated translation initiation machinery.
Authors: Jeong, S.J. / Park, S. / Nguyen, L.T. / Hwang, J. / Lee, E.Y. / Giong, H.K. / Lee, J.S. / Yoon, I. / Lee, J.H. / Kim, J.H. / Kim, H.K. / Kim, D. / Yang, W.S. / Kim, S.Y. / Lee, C.Y. / Yu, K. ...Authors: Jeong, S.J. / Park, S. / Nguyen, L.T. / Hwang, J. / Lee, E.Y. / Giong, H.K. / Lee, J.S. / Yoon, I. / Lee, J.H. / Kim, J.H. / Kim, H.K. / Kim, D. / Yang, W.S. / Kim, S.Y. / Lee, C.Y. / Yu, K. / Sonenberg, N. / Kim, M.H. / Kim, S.
History
DepositionMay 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E type 2
B: Threonine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)27,0512
Polymers27,0512
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-11 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.369, 60.569, 85.237
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 4E type 2 / eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic ...eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic translation initiation factor 4E-like 3 / eIF4E-like protein 4E-LP / mRNA cap-binding protein 4EHP / h4EHP / mRNA cap-binding protein type 3


Mass: 21963.121 Da / Num. of mol.: 1 / Fragment: UNP residues 45-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E2, EIF4EL3 / Production host: Escherichia coli (E. coli) / References: UniProt: O60573
#2: Protein/peptide Threonine--tRNA ligase, cytoplasmic / Threonyl-tRNA synthetase / ThrRS


Mass: 5087.679 Da / Num. of mol.: 1 / Fragment: UNP residues 30-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARS / Production host: Escherichia coli (E. coli) / References: UniProt: P26639, threonine-tRNA ligase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 20% PEG 8000, 0.1 M CHES (pH 9.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 20718 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 21.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 1.9→25.815 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.44
RfactorNum. reflection% reflection
Rfree0.1964 1064 5.14 %
Rwork0.161 --
obs0.1628 20715 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→25.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 0 177 1754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071619
X-RAY DIFFRACTIONf_angle_d0.9922191
X-RAY DIFFRACTIONf_dihedral_angle_d13.951596
X-RAY DIFFRACTIONf_chiral_restr0.045230
X-RAY DIFFRACTIONf_plane_restr0.004278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8967-1.9830.21871260.18282321X-RAY DIFFRACTION97
1.983-2.08750.23191310.15592435X-RAY DIFFRACTION100
2.0875-2.21830.17741270.1562431X-RAY DIFFRACTION100
2.2183-2.38940.19621250.16532446X-RAY DIFFRACTION100
2.3894-2.62970.20081660.16532430X-RAY DIFFRACTION100
2.6297-3.00970.21341270.16532467X-RAY DIFFRACTION100
3.0097-3.790.18951180.15072537X-RAY DIFFRACTION100
3.79-25.81690.18831440.16312584X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.0946 Å / Origin y: -18.8482 Å / Origin z: -14.7696 Å
111213212223313233
T0.1465 Å20.0078 Å2-0.0023 Å2-0.1432 Å2-0.0129 Å2--0.1214 Å2
L1.2716 °20.1117 °20.055 °2-1.3353 °2-0.0308 °2--0.5538 °2
S-0.0262 Å °0.0406 Å °-0.0116 Å °-0.0164 Å °0.0103 Å °-0.0285 Å °0.0066 Å °-0.0013 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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