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- PDB-5a1n: The crystal structure of the GST-like domains complex of EPRS-AIM... -

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Basic information

Entry
Database: PDB / ID: 5a1n
TitleThe crystal structure of the GST-like domains complex of EPRS-AIMP2 mutant S156D
Components
  • AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
  • BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
KeywordsLIGASE / AIMP2 / EPRS / GST-LIKE DOMAIN
Function / homology
Function and homology information


type II pneumocyte differentiation / regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / Selenoamino acid metabolism / glutamate-tRNA ligase activity / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol ...type II pneumocyte differentiation / regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / Selenoamino acid metabolism / glutamate-tRNA ligase activity / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / GAIT complex / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of protein ubiquitination / cellular response to type II interferon / cellular response to insulin stimulus / RNA stem-loop binding / GTPase binding / protein-containing complex assembly / molecular adaptor activity / negative regulation of translation / protein ubiquitination / translation / ribonucleoprotein complex / negative regulation of cell population proliferation / apoptotic process / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / WHEP-TRS domain / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Glutathione S-transferase, C-terminal domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Glutathione S-transferase, C-terminal domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / S15/NS1, RNA-binding / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bifunctional glutamate/proline--tRNA ligase / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCho, H.Y. / Choi, Y.S. / Kang, B.S.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Symmetric Assembly of a Decameric Subcomplex in Human Multi-tRNA Synthetase Complex Via Interactions between Glutathione Transferase-Homology Domains and Aspartyl-tRNA Synthetase.
Authors: Cho, H.Y. / Lee, H.J. / Choi, Y.S. / Kim, D.K. / Jin, K.S. / Kim, S. / Kang, B.S.
History
DepositionMay 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
B: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3144
Polymers46,1302
Non-polymers1842
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-13.5 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.619, 75.619, 175.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE / BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE / CELL PROLIFERATION-INDUCING GENE 32 PROTEIN / GLUTAMATYL- ...BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE / CELL PROLIFERATION-INDUCING GENE 32 PROTEIN / GLUTAMATYL-PROLYL-TRNA SYNTHETASE / GLUTAMYL-TRNA SYNTHETASE / GLURS / PROLYL-TRNA SYNTHETASE / GLUTAMYL-PROLY L-TRNA SYNTHETASE


Mass: 19310.699 Da / Num. of mol.: 1 / Fragment: GST-LIKE DOMAIN, RESIDUES 1-175 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: M1 TO R175 OF EPRS GST-LIKE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07814, proline-tRNA ligase, glutamate-tRNA ligase
#2: Protein AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2 / MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P38 / PROTEIN JTV-1 / AMINOACYL TRNA SYNTHASE COMPLEX- ...MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P38 / PROTEIN JTV-1 / AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN


Mass: 26818.926 Da / Num. of mol.: 1 / Fragment: GST-LIKE DOMAIN, RESIDUES 90-320 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: T90 TO K320 OF AIMP2 GST-LIKE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13155
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.73 Å3/Da / Density % sol: 55.01 % / Description: NONE
Crystal growpH: 5.5 / Details: 17% PEG 3350, 0.1M BIS-TRIS PH 5.5, 2MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 30430 / % possible obs: 99.3 % / Observed criterion σ(I): -2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 41
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TO BE PUBLISHED

Resolution: 2.1→46.323 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1999 6.6 %
Rwork0.1933 --
obs0.1958 30347 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 12 199 3071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072975
X-RAY DIFFRACTIONf_angle_d1.0474051
X-RAY DIFFRACTIONf_dihedral_angle_d13.6211041
X-RAY DIFFRACTIONf_chiral_restr0.042477
X-RAY DIFFRACTIONf_plane_restr0.004511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1016-2.15420.32191370.23821939X-RAY DIFFRACTION98
2.1542-2.21240.2761410.23331994X-RAY DIFFRACTION100
2.2124-2.27750.27671410.22312016X-RAY DIFFRACTION100
2.2775-2.3510.26431410.2211996X-RAY DIFFRACTION100
2.351-2.4350.23531420.21862012X-RAY DIFFRACTION100
2.435-2.53250.26171410.21361986X-RAY DIFFRACTION100
2.5325-2.64780.2791420.21712014X-RAY DIFFRACTION100
2.6478-2.78740.2511430.21352025X-RAY DIFFRACTION100
2.7874-2.9620.22521410.21282021X-RAY DIFFRACTION100
2.962-3.19060.25361460.20952048X-RAY DIFFRACTION100
3.1906-3.51160.20281440.19482048X-RAY DIFFRACTION100
3.5116-4.01950.2161460.17382076X-RAY DIFFRACTION100
4.0195-5.06310.22281480.15442099X-RAY DIFFRACTION100
5.0631-46.33410.19591460.18582074X-RAY DIFFRACTION92

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