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- PDB-6iy6: Crystal structure of human cytosolic aspartyl-tRNA synthetase (DR... -

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Basic information

Entry
Database: PDB / ID: 6iy6
TitleCrystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) in complex with glutathion-S transferase (GST) domains from Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2) and glutamyl-prolyl-tRNA synthetase (EPRS)
Components
  • Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
  • Aspartate--tRNA ligase, cytoplasmic
  • Bifunctional glutamate/proline--tRNA ligase
KeywordsTRANSLATION / Aminoacyl-tRNA transferase Glutathion-S transferase domain
Function / homology
Function and homology information


aspartate-tRNA ligase / aminoacylase activity / regulation of long-chain fatty acid import into cell / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / type II pneumocyte differentiation / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation ...aspartate-tRNA ligase / aminoacylase activity / regulation of long-chain fatty acid import into cell / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / type II pneumocyte differentiation / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / 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 / RNA stem-loop binding / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / 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 / synapse / protein homodimerization activity / RNA binding / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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 / Aspartate-tRNA synthetase, type 2 / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / : ...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 / Aspartate-tRNA synthetase, type 2 / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / : / 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 (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / OB-fold nucleic acid binding domain / Anticodon-binding / Anticodon binding domain / Glutathione S-transferase, C-terminal 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 / Nucleic acid-binding, OB-fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Bifunctional glutamate/proline--tRNA ligase / Aspartate--tRNA ligase, cytoplasmic / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsPark, S.H. / Hahn, H. / Han, B.W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2011-0030001 Korea, Republic Of
National Research Foundation (Korea)NRF-2013M-3A6A-4043695 Korea, Republic Of
CitationJournal: Iucrj / Year: 2019
Title: The DRS-AIMP2-EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex.
Authors: Hahn, H. / Park, S.H. / Kim, H.J. / Kim, S. / Han, B.W.
History
DepositionDec 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Aspartate--tRNA ligase, cytoplasmic
B: Aspartate--tRNA ligase, cytoplasmic
C: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
D: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
E: Bifunctional glutamate/proline--tRNA ligase
F: Bifunctional glutamate/proline--tRNA ligase
G: Aspartate--tRNA ligase, cytoplasmic
H: Aspartate--tRNA ligase, cytoplasmic
I: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
J: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
K: Bifunctional glutamate/proline--tRNA ligase
L: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,38531
Polymers399,64012
Non-polymers1,74519
Water21612
1
A: Aspartate--tRNA ligase, cytoplasmic
B: Aspartate--tRNA ligase, cytoplasmic
C: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
D: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
E: Bifunctional glutamate/proline--tRNA ligase
F: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,02519
Polymers199,8206
Non-polymers1,20513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18630 Å2
ΔGint-157 kcal/mol
Surface area68010 Å2
MethodPISA
2
G: Aspartate--tRNA ligase, cytoplasmic
H: Aspartate--tRNA ligase, cytoplasmic
I: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
J: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
K: Bifunctional glutamate/proline--tRNA ligase
L: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,36012
Polymers199,8206
Non-polymers5406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17050 Å2
ΔGint-109 kcal/mol
Surface area67540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.068, 108.068, 815.642
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 3 types, 12 molecules ABGHCDIJEFKL

#1: Protein
Aspartate--tRNA ligase, cytoplasmic / Aspartyl-tRNA synthetase / AspRS / Cell proliferation-inducing gene 40 protein


Mass: 57310.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DARS, PIG40 / Production host: Escherichia coli (E. coli) / References: UniProt: P14868, aspartate-tRNA ligase
#2: Protein
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Multisynthase complex auxiliary component p38 / Protein JTV-1


Mass: 24165.006 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP2, JTV1, PRO0992 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13155
#3: 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


Mass: 18434.824 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli)
References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase

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Non-polymers , 3 types, 31 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M CAPS (pH 10.5) 1.3 M sodium phosphate monobasic 0.5 M potassium phosphate dibasic 0.5 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 61327 / % possible obs: 98.7 % / Redundancy: 2.9 % / Rsym value: 0.103 / Net I/σ(I): 8.18
Reflection shellResolution: 3.6→3.66 Å / Num. unique obs: 2998 / Rsym value: 0.772

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J15, 5A34

4j15

5a34


Resolution: 3.6→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2754 3073 -
Rwork0.2367 --
obs0.2386 60959 98.54 %
Refinement stepCycle: LAST / Resolution: 3.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24440 0 87 12 24539
LS refinement shellResolution: 3.6→3.7286 Å
RfactorNum. reflection% reflection
Rfree0.3318 --
Rwork0.3462 --
obs-5759 99.5 %

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