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- PDB-4r3z: Crystal structure of human ArgRS-GlnRS-AIMP1 complex -

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Basic information

Entry
Database: PDB / ID: 4r3z
TitleCrystal structure of human ArgRS-GlnRS-AIMP1 complex
Components
  • Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
  • Arginine--tRNA ligase, cytoplasmic
  • Glutamine--tRNA ligase
KeywordsPROTEIN BINDING/LIGASE / Amino-acyl tRNA synthetase complex / multi-synthetase complex / Ligation Amino acid to tRNA / PROTEIN BINDING-LIGASE complex
Function / homology
Function and homology information


arginine-tRNA ligase / glutamine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / positive regulation of glucagon secretion / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation ...arginine-tRNA ligase / glutamine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / positive regulation of glucagon secretion / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / arginine binding / negative regulation of stress-activated MAPK cascade / leukocyte migration / mitochondrial translation / protein kinase inhibitor activity / negative regulation of endothelial cell proliferation / negative regulation of apoptotic signaling pathway / cytokine activity / negative regulation of protein kinase activity / brain development / GTPase binding / cell-cell signaling / angiogenesis / defense response to virus / tRNA binding / mitochondrial matrix / cadherin binding / inflammatory response / translation / negative regulation of DNA-templated transcription / apoptotic process / nucleolus / protein kinase binding / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 / Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily ...Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 / Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / Glutamine-tRNA synthetase / DALR anticodon binding / DALR anticodon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / 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 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Glutamine--tRNA ligase / Arginine--tRNA ligase, cytoplasmic / Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.033 Å
AuthorsFu, Y. / Kim, Y. / Cho, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of the ArgRS-GlnRS-AIMP1 complex and its implications for mammalian translation
Authors: Fu, Y. / Kim, Y. / Jin, K.S. / Kim, H.S. / Kim, J.H. / Wang, D.M. / Park, M. / Jo, C.H. / Kwon, N.H. / Kim, D. / Kim, M.H. / Jeon, Y.H. / Hwang, K.Y. / Kim, S. / Cho, Y.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Structure summary
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Arginine--tRNA ligase, cytoplasmic
C: Glutamine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)202,1553
Polymers202,1553
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.645, 313.253, 161.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 / Multisynthase complex auxiliary component p43 / Endothelial monocyte-activating polypeptide 2 / ...Multisynthase complex auxiliary component p43 / Endothelial monocyte-activating polypeptide 2 / EMAP-2 / Endothelial monocyte-activating polypeptide II / EMAP-II / Small inducible cytokine subfamily E member 1


Mass: 34404.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP1, EMAP2, SCYE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12904
#2: Protein Arginine--tRNA ligase, cytoplasmic / Arginyl-tRNA synthetase / ArgRS


Mass: 77230.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARS / Production host: Escherichia coli (E. coli) / References: UniProt: P54136, arginine-tRNA ligase
#3: Protein Glutamine--tRNA ligase / Glutaminyl-tRNA synthetase / GlnRS


Mass: 90519.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QARS / Production host: Escherichia coli (E. coli) / References: UniProt: P47897, glutamine-tRNA ligase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 5-10% Methyl-pentene-Diol, 0.1M tris-HCl(pH7.4), 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2013
RadiationMonochromator: Si 4-crystal channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 20581 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 102.66 Å2
Reflection shellResolution: 3.85→3.92 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1745)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.033→37.916 Å / SU ML: 0.54 / σ(F): 1.35 / Phase error: 34.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 765 4.98 %
Rwork0.2293 14602 -
obs0.2321 15367 70.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 328.31 Å2 / Biso mean: 153.5618 Å2 / Biso min: 48.08 Å2
Refinement stepCycle: LAST / Resolution: 4.033→37.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10242 0 0 0 10242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510455
X-RAY DIFFRACTIONf_angle_d0.96114114
X-RAY DIFFRACTIONf_chiral_restr0.0371554
X-RAY DIFFRACTIONf_plane_restr0.0051820
X-RAY DIFFRACTIONf_dihedral_angle_d16.63949
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0333-4.34430.4402610.31931095115627
4.3443-4.78070.32111010.26362068216950
4.7807-5.47080.36231550.25823114326975
5.4708-6.88580.34652320.28294062429498
6.8858-37.91820.20872160.1794263447999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7225-2.86210.54326.9981-1.00430.0475-1.5261-0.8240.0188-0.55722.31442.0574-0.4757-1.15830.7791.59830.4002-0.66581.39210.20971.146911.56154.433541.601
24.7418-0.85860.39410.17950.18924.86420.6117-0.7207-0.39270.8151-0.0288-1.7725-0.59540.56310.65990.5287-0.3978-0.72051.1259-0.2061.8054-8.200145.376326.7301
31.9994-0.54832.00238.1916-0.69726.64030.8746-3.4833-1.9595-0.04880.49060.38340.0901-0.94281.7470.5961-0.2174-0.07251.1941-0.57092.4275-24.390758.814124.5116
40.04052.24150.47055.77641.2412-0.0748-0.04770.057-0.5118-0.2396-0.1387-0.534-0.37550.37370.2121.0940.4815-0.16011.6466-0.07961.0763-6.266246.86220.4651
51.7193-0.4450.02294.49333.12214.2987-0.0934-0.45350.11540.481-0.41231.3519-0.3168-0.41810.78991.141-0.06210.11560.9036-0.12661.0171-22.719189.315647.4614
63.7166-0.5371-0.57692.4997-0.14484.4053-0.00020.64860.7386-0.5391-0.28290.5136-0.57780.25270.19771.7514-0.0185-0.25680.8187-0.02330.8957-15.671887.888619.3356
70.5891.19590.67975.19540.13192.7933-0.5228-0.0969-0.17340.8501-0.11291.4693-1.216-1.008-0.54070.2615-0.05510.29591.4123-0.34551.3759-43.71523.334314.0996
89.2665-3.9694.99134.1921-1.41082.88240.519-2.5254-0.00281.4221.8119-0.7302-0.09-0.3350.29412.77510.70110.22752.1464-0.84881.1046-36.189543.927535.7748
95.29190.9993-0.34497.15172.81534.1287-0.2882-0.63420.54661.395-0.61671.01470.0628-0.49750.67641.02040.1492-0.28291.0098-0.46881.1487-32.109739.182924.1994
100.9649-0.3912-0.77937.0937.18217.2478-0.3420.55390.37342.06890.50550.71811.3184-1.38942.12040.61040.31780.471.4214-0.65682.0111-48.340628.69222.0797
112.6577-0.1312-0.21955.23480.11222.73290.1324-0.4085-0.30260.1436-0.1550.30040.224-0.28710.04430.4322-0.22550.06170.913-0.01860.7337-31.1218-17.76417.2313
122.5402-1.23191.6645.78682.65043.72940.1847-0.6663-0.86611.2093-0.3103-0.03990.55240.04110.15740.6425-0.24660.03841.04690.14110.5672-28.2084-8.588121.4134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:43 )A5 - 43
2X-RAY DIFFRACTION2chain 'A' and (resseq 44:69 )A44 - 69
3X-RAY DIFFRACTION3chain 'A' and (resseq 70:80 )A70 - 80
4X-RAY DIFFRACTION4chain 'B' and (resseq 2:177 )B2 - 177
5X-RAY DIFFRACTION5chain 'B' and (resseq 178:376 )B178 - 376
6X-RAY DIFFRACTION6chain 'B' and (resseq 377:660 )B377 - 660
7X-RAY DIFFRACTION7chain 'C' and (resseq 220:351 )C220 - 351
8X-RAY DIFFRACTION8chain 'C' and (resseq 352:379 )C352 - 379
9X-RAY DIFFRACTION9chain 'C' and (resseq 380:448 )C380 - 448
10X-RAY DIFFRACTION10chain 'C' and (resseq 449:483 )C449 - 483
11X-RAY DIFFRACTION11chain 'C' and (resseq 484:690 )C484 - 690
12X-RAY DIFFRACTION12chain 'C' and (resseq 691:771 )C691 - 771

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