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- PDB-5y6l: A subcomplex crystal structure of human cytosolic aspartyl-tRNA s... -

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Basic information

Entry
Database: PDB / ID: 5y6l
TitleA subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex
Components
  • Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
  • Aspartate--tRNA ligase, cytoplasmic
  • Bifunctional glutamate/proline--tRNA ligase
  • Eukaryotic translation elongation factor 1 epsilon-1
  • Methionine--tRNA ligase, cytoplasmic
KeywordsLIGASE / AMINO-ACYL TRNA SYNTHETASE COMPLEX / MULTI-SYNTHETASE COMPLEX / LIGATION AMINO ACID TO TRNA
Function / homology
Function and homology information


type II pneumocyte differentiation / aspartate-tRNA ligase / aminoacylase activity / regulation of long-chain fatty acid import into cell / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / glutamate-tRNA ligase / Selenoamino acid metabolism / glutamate-tRNA ligase activity / proline-tRNA ligase ...type II pneumocyte differentiation / aspartate-tRNA ligase / aminoacylase activity / regulation of long-chain fatty acid import into cell / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / glutamate-tRNA ligase / Selenoamino acid metabolism / glutamate-tRNA ligase activity / proline-tRNA ligase / methionine-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / rRNA transcription / cellular response to platelet-derived growth factor stimulus / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to epidermal growth factor stimulus / cellular response to leukemia inhibitory factor / positive regulation of apoptotic signaling pathway / positive regulation of protein ubiquitination / cellular response to type II interferon / cellular response to insulin stimulus / RNA stem-loop binding / positive regulation of cellular senescence / GTPase binding / protein-containing complex assembly / molecular adaptor activity / tRNA binding / negative regulation of translation / protein ubiquitination / positive regulation of apoptotic process / translation / ribonucleoprotein complex / negative regulation of cell population proliferation / apoptotic process / synapse / nucleolus / protein homodimerization activity / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal 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 ...Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal 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 / Aspartate-tRNA synthetase, type 2 / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / 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 / Anticodon binding domain of methionyl tRNA ligase / 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 / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / 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) / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding 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 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / 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 / Glutaredoxin / Glutaredoxin / S15/NS1, RNA-binding / Nucleic acid-binding, OB-fold / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Eukaryotic translation elongation factor 1 epsilon-1 / Bifunctional glutamate/proline--tRNA ligase / Aspartate--tRNA ligase, cytoplasmic / Methionine--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: 2.9 Å
AuthorsCho, H.Y. / Lee, H.J. / Kang, B.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research FoundationNRF-2014M3A6A4062857 Korea, Republic Of
CitationJournal: To be published
Title: A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex
Authors: Cho, H.Y. / Lee, H.J. / Kang, B.S.
History
DepositionAug 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: Methionine--tRNA ligase, cytoplasmic
B: Eukaryotic translation elongation factor 1 epsilon-1
C: Bifunctional glutamate/proline--tRNA ligase
D: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
E: Aspartate--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,8587
Polymers152,6685
Non-polymers1902
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-53 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.535, 98.413, 125.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 5 types, 5 molecules ABCDE

#1: Protein Methionine--tRNA ligase, cytoplasmic / Methionyl-tRNA synthetase / MetRS


Mass: 25956.354 Da / Num. of mol.: 1 / Fragment: UNP residues 1-224, MRS N-TERMINUS DOMAIN / Mutation: S171R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARS / Production host: Escherichia coli (E. coli) / References: UniProt: P56192, methionine-tRNA ligase
#2: Protein Eukaryotic translation elongation factor 1 epsilon-1 / Aminoacyl tRNA synthetase complex-interacting multifunctional protein 3 / Elongation factor p18 / ...Aminoacyl tRNA synthetase complex-interacting multifunctional protein 3 / Elongation factor p18 / Multisynthase complex auxiliary component p18


Mass: 21226.016 Da / Num. of mol.: 1
Fragment: AIMP3 WITH ADDITIONAL S SEQUENCE AT THE N-TERMINUS
Mutation: C147S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1E1, AIMP3, P18 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43324
#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: 19310.699 Da / Num. of mol.: 1 / Fragment: UNP residues 1-175, EPRS GST-LIKE DOMAIN / Mutation: C92S, C105S, C123S
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
#4: Protein Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Multisynthase complex auxiliary component p38 / Protein JTV-1


Mass: 26790.916 Da / Num. of mol.: 1 / Fragment: UNP residues 90-320, AIMP2 GST-LIKE DOMAIN
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
#5: Protein Aspartate--tRNA ligase, cytoplasmic / Aspartyl-tRNA synthetase / AspRS / Cell proliferation-inducing gene 40 protein


Mass: 59384.441 Da / Num. of mol.: 1
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

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Non-polymers , 2 types, 80 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.72 Å3/Da / Density % sol: 28.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 3000 Na/K phosphate pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 24317 / % possible obs: 99.5 % / Redundancy: 6.8 % / Net I/σ(I): 17.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2376 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BVY, 5BMU, 5A34

4bvy

5bmu

5a34


Resolution: 2.9→29.873 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.98
RfactorNum. reflection% reflection
Rfree0.2518 1962 8.23 %
Rwork0.1765 --
obs0.1828 23831 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6370 0 10 78 6458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016523
X-RAY DIFFRACTIONf_angle_d1.0758887
X-RAY DIFFRACTIONf_dihedral_angle_d16.1563864
X-RAY DIFFRACTIONf_chiral_restr0.0551033
X-RAY DIFFRACTIONf_plane_restr0.0071126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.97260.36181390.26241548X-RAY DIFFRACTION100
2.9726-3.05290.37821350.26631513X-RAY DIFFRACTION100
3.0529-3.14260.36231400.25081555X-RAY DIFFRACTION100
3.1426-3.2440.33531380.2261530X-RAY DIFFRACTION100
3.244-3.35980.3011360.22261524X-RAY DIFFRACTION100
3.3598-3.49410.29111400.19951561X-RAY DIFFRACTION100
3.4941-3.65280.25181390.16651542X-RAY DIFFRACTION100
3.6528-3.8450.22361400.16561564X-RAY DIFFRACTION100
3.845-4.08540.2561400.16481550X-RAY DIFFRACTION100
4.0854-4.39990.2061380.14861551X-RAY DIFFRACTION100
4.3999-4.8410.26591420.14031572X-RAY DIFFRACTION100
4.841-5.53770.20031420.15381591X-RAY DIFFRACTION100
5.5377-6.96230.22341450.19411603X-RAY DIFFRACTION100
6.9623-29.87480.22161480.15681665X-RAY DIFFRACTION99

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