[English] 日本語
Yorodumi
- PDB-5a34: The crystal structure of the GST-like domains complex of EPRS-AIMP2 -

+
Open data


ID or keywords:

Loading...

-
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 / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex ...type II pneumocyte differentiation / regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / 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 / 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 / cytosol / cytoplasm
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 / : / Nuclear-export cofactor Arc1p / 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 / : / Nuclear-export cofactor Arc1p / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more