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- PDB-8j9s: leucine zipper complex of AIMP1 and AIMP2 -

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Basic information

Entry
Database: PDB / ID: 8j9s
Titleleucine zipper complex of AIMP1 and AIMP2
Components
  • Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
  • Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
KeywordsTRANSLATION / aminoacyl-tRNA synthetase
Function / homology
Function and homology information


positive regulation of glucagon secretion / type II pneumocyte differentiation / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of protein ubiquitination / cytokine activity ...positive regulation of glucagon secretion / type II pneumocyte differentiation / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of protein ubiquitination / cytokine activity / cell-cell signaling / positive regulation of neuron apoptotic process / GTPase binding / protein-containing complex assembly / angiogenesis / defense response to virus / molecular adaptor activity / tRNA binding / protein ubiquitination / translation / inflammatory response / negative regulation of cell population proliferation / apoptotic process / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / nucleus / membrane / 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 / : / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Glutathione S-transferase, C-terminal 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 / : / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
IODIDE ION / Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsKim, D.K. / Kang, B.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2C1003541 Korea, Republic Of
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Assembly of the Human Multi-tRNA Synthetase Complex Through Leucine Zipper Motifs.
Authors: Kim, D.K. / Lee, K. / Kang, B.S.
History
DepositionMay 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
B: Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
C: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5528
Polymers23,9183
Non-polymers6355
Water00
1
A: Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
hetero molecules

B: Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
C: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5528
Polymers23,9183
Non-polymers6355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z+1/41
Buried area4290 Å2
ΔGint-31 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.445, 95.445, 74.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
DetailsOther experimental results indicate that AIMP1 interacts both AIMP1 and AIMP2 through its C-and N-terminal parts, respectively.

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Components

#1: Protein Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 / Multisynthase complex auxiliary component p43


Mass: 9124.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12904
#2: Protein/peptide Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Multisynthase complex auxiliary component p38 / Protein JTV-1


Mass: 5668.402 Da / Num. of mol.: 1
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: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
Has ligand of interestN
Has protein modificationN

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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: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 62% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7226 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 28.13 Å2 / CC1/2: 1 / Net I/σ(I): 19.8
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 346 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→34.66 Å / SU ML: 0.408 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 25.7525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2731 652 10 %
Rwork0.2324 5871 -
obs0.2366 6523 90.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.23 Å2
Refinement stepCycle: LAST / Resolution: 3.01→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 5 0 1380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231375
X-RAY DIFFRACTIONf_angle_d0.47321828
X-RAY DIFFRACTIONf_chiral_restr0.0297218
X-RAY DIFFRACTIONf_plane_restr0.0017232
X-RAY DIFFRACTIONf_dihedral_angle_d4.3703178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.240.3426820.2875726X-RAY DIFFRACTION57.92
3.24-3.570.33291360.25721220X-RAY DIFFRACTION95.83
3.57-4.080.25041390.23351247X-RAY DIFFRACTION97.88
4.08-5.140.2491430.2051291X-RAY DIFFRACTION99.31
5.14-34.660.24831520.22241387X-RAY DIFFRACTION99.81

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