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- PDB-5a34: The crystal structure of the GST-like domains complex of EPRS-AIMP2 -

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Basic information

Entry
Database: PDB / ID: 5a34
TitleThe crystal structure of the GST-like domains complex of EPRS-AIMP2
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 / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol ...type II pneumocyte differentiation / regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / GAIT complex / positive regulation of protein ubiquitination / cellular response to type II interferon / RNA stem-loop binding / cellular response to insulin stimulus / GTPase binding / protein-containing complex assembly / molecular adaptor activity / negative regulation of translation / protein ubiquitination / ribonucleoprotein complex / translation / negative regulation of cell population proliferation / apoptotic process / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain ...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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / 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) / 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 / 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: 2.6 Å
AuthorsCho, H.Y. / Kang, B.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Assembly of Multi-tRNA Synthetase Complex Via Heterotetrameric Glutathione Transferase-Homology Domains.
Authors: Cho, H.Y. / Maeng, S.J. / Cho, H.J. / Choi, Y.S. / Chung, J.M. / Lee, S. / Kim, H.K. / Kim, J.H. / Eom, C. / Kim, Y. / Guo, M. / Jung, H.S. / Kang, B.S. / Kim, S.
History
DepositionMay 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Jan 10, 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

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Assembly

Deposited unit
A: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
B: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
C: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
D: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
E: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
F: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
G: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
H: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,78310
Polymers184,5998
Non-polymers1842
Water1,20767
1
A: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
B: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2423
Polymers46,1502
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-16.1 kcal/mol
Surface area17400 Å2
MethodPISA
2
E: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
F: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)46,1502
Polymers46,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-14.8 kcal/mol
Surface area16920 Å2
MethodPISA
3
G: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
H: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)46,1502
Polymers46,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-14.4 kcal/mol
Surface area16710 Å2
MethodPISA
4
C: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
D: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2423
Polymers46,1502
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-15 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.669, 111.767, 181.253
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
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


Mass: 19358.895 Da / Num. of mol.: 4 / Fragment: GST-LIKE DOMAIN, UNP RESIDUES 1-175
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


Mass: 26790.916 Da / Num. of mol.: 4 / Fragment: GST-LIKE DOMAIN, 90-320
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.: 67 / 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: 2.61 Å3/Da / Density % sol: 52.83 % / Description: NONE
Crystal growpH: 7.5 / Details: PEG 3350 22% , 0.2 M AMMONIUM CHLORIDE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 12, 2014 / Details: VERTICAL FOCUSING TOROIDAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 59779 / % possible obs: 99.7 % / Observed criterion σ(I): -2 / Redundancy: 6.6 % / Biso Wilson estimate: 57.37 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 17.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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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: PB ENTRY 5BMU

5bmu


Resolution: 2.6→42.503 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1998 3.3 %
Rwork0.1886 --
obs0.1905 59630 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→42.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11163 0 12 67 11242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911454
X-RAY DIFFRACTIONf_angle_d1.20115604
X-RAY DIFFRACTIONf_dihedral_angle_d15.143961
X-RAY DIFFRACTIONf_chiral_restr0.0461868
X-RAY DIFFRACTIONf_plane_restr0.0051955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.66510.32291390.26294027X-RAY DIFFRACTION98
2.6651-2.73710.27341410.23924053X-RAY DIFFRACTION100
2.7371-2.81770.28861420.23584090X-RAY DIFFRACTION100
2.8177-2.90860.34031420.23354084X-RAY DIFFRACTION100
2.9086-3.01250.29771410.23874082X-RAY DIFFRACTION100
3.0125-3.13310.29751420.2314094X-RAY DIFFRACTION100
3.1331-3.27560.31851420.21944108X-RAY DIFFRACTION100
3.2756-3.44830.28751420.20514083X-RAY DIFFRACTION100
3.4483-3.66420.24971430.19794133X-RAY DIFFRACTION100
3.6642-3.94690.25541430.18444141X-RAY DIFFRACTION100
3.9469-4.34380.18561430.1594123X-RAY DIFFRACTION100
4.3438-4.97150.20791440.15454173X-RAY DIFFRACTION100
4.9715-6.26030.24371470.18944214X-RAY DIFFRACTION100
6.2603-42.50910.22141470.16024227X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -13.0105 Å / Origin y: 111.4648 Å / Origin z: 90.1537 Å
111213212223313233
T0.4113 Å20.0108 Å20.0244 Å2-0.4142 Å20.0408 Å2--0.4854 Å2
L0.2544 °20.0215 °2-0.0468 °2-0.0135 °20.0065 °2--0.4738 °2
S-0.0817 Å °-0.0374 Å °0.0328 Å °0.0153 Å °-0.0343 Å °0.0268 Å °-0.0345 Å °0.0004 Å °0.1174 Å °
Refinement TLS groupSelection details: ALL

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