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- PDB-6ild: Crystal Structure of Human LysRS: P38/AIMP2 Complex II -

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Basic information

Entry
Database: PDB / ID: 6ild
TitleCrystal Structure of Human LysRS: P38/AIMP2 Complex II
Components
  • Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
  • Lysine--tRNA ligase
KeywordsLIGASE / lysyl-tRNA synthetase / LysRS / P38 / AIMP2 / multi tRNA synthetase complex sub-complex
Function / homology
Function and homology information


type II pneumocyte differentiation / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / Selenoamino acid metabolism / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process ...type II pneumocyte differentiation / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / Selenoamino acid metabolism / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / ERK1 and ERK2 cascade / positive regulation of protein ubiquitination / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein-containing complex assembly / tRNA binding / molecular adaptor activity / protein ubiquitination / mitochondrial matrix / translation / negative regulation of cell population proliferation / apoptotic process / positive regulation of DNA-templated transcription / protein homodimerization activity / mitochondrion / extracellular space / ATP binding / identical protein binding / membrane / nucleus / plasma 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 / Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) ...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 / Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Glutathione S-transferase, C-terminal domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Glutathione S-transferase, C-terminal / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Glutathione S-transferase, C-terminal domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine / LYSINE / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Lysine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.882 Å
AuthorsHei, Z. / Liu, Z. / Wang, J. / Fang, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21778064 China
National Natural Science Foundation of China21778067 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex.
Authors: Hei, Z. / Wu, S. / Liu, Z. / Wang, J. / Fang, P.
History
DepositionOct 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)124,78313
Polymers123,6343
Non-polymers1,14910
Water16,394910
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint-76 kcal/mol
Surface area41710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.511, 100.074, 270.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1056-

HOH

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 59240.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KARS, KIAA0070 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15046, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, lysine-tRNA ligase
#2: Protein/peptide Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Multisynthase complex auxiliary component p38


Mass: 5153.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13155

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Non-polymers , 5 types, 920 molecules

#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-45A / 5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine


Type: RNA linking / Mass: 345.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N5O6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8 % PEG 20000, 0.1 M Tris pH 8.0, 0.1 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 104488 / % possible obs: 98.5 % / Redundancy: 7.9 % / Biso Wilson estimate: 20.78 Å2 / Rmerge(I) obs: 0.068 / Χ2: 0.941 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.88-1.957.50.571101970.817197.6
1.95-2.038.10.393103300.844198.3
2.03-2.128.10.276103630.914198.4
2.12-2.238.10.191103750.931198.7
2.23-2.378.10.145104040.977198.8
2.37-2.558.10.114104671.044198.9
2.55-2.818.10.083104691.043199.1
2.81-3.2180.056105741.002199.3
3.21-4.057.80.041106051.172199
4.05-507.30.026107040.632197.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BJU

3bju


Resolution: 1.882→32.42 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 17.54
RfactorNum. reflection% reflection
Rfree0.1844 5048 4.99 %
Rwork0.1535 --
obs0.155 101191 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.16 Å2 / Biso mean: 27.0836 Å2 / Biso min: 9.43 Å2
Refinement stepCycle: final / Resolution: 1.882→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8197 0 75 910 9182
Biso mean--36.95 36.02 -
Num. residues----1030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.882-1.90340.28281050.21542057216263
1.9034-1.92580.24711370.20582508264574
1.9258-1.94930.23961290.18742760288984
1.9493-1.9740.20461620.17232941310388
1.974-1.99990.221680.17173009317791
1.9999-2.02730.22461820.1683090327294
2.0273-2.05630.18581620.16253293345597
2.0563-2.0870.18631700.15923253342398
2.087-2.11960.20731910.16343252344398
2.1196-2.15430.21281410.1573316345798
2.1543-2.19150.19671670.16033310347799
2.1915-2.23130.21241650.15913282344799
2.2313-2.27420.21081680.15633290345899
2.2742-2.32060.19532000.15463318351899
2.3206-2.37110.18611830.15133243342699
2.3711-2.42620.17871800.15633305348599
2.4262-2.48680.21711830.15453308349199
2.4868-2.55410.19161800.1553303348399
2.5541-2.62920.21171690.15723314348399
2.6292-2.7140.21631870.16193320350799
2.714-2.8110.18451780.15893317349599
2.811-2.92340.19141930.16233332352599
2.9234-3.05640.20411680.16123344351299
3.0564-3.21740.20021670.15993375354299
3.2174-3.41880.18991590.15823366352599
3.4188-3.68240.18281790.15083366354599
3.6824-4.05230.15851560.13173378353498
4.0523-4.63730.1341790.11963361354098
4.6373-5.83690.13951610.14043392355398
5.8369-32.42490.15721790.16273440361996
Refinement TLS params.Method: refined / Origin x: -2.6964 Å / Origin y: 7.159 Å / Origin z: 30.6284 Å
111213212223313233
T0.1283 Å2-0.0435 Å2-0.0168 Å2-0.1353 Å20.013 Å2--0.1169 Å2
L0.3255 °2-0.0498 °2-0.0584 °2-0.5147 °20.2752 °2--0.534 °2
S-0.0222 Å °-0.0132 Å °0.0163 Å °0.0916 Å °0.0003 Å °-0.0176 Å °0.1476 Å °-0.0344 Å °0.0103 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA72 - 576
2X-RAY DIFFRACTION1allB72 - 575
3X-RAY DIFFRACTION1allC2 - 31
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allH2 - 1347
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allI1
9X-RAY DIFFRACTION1allJ1
10X-RAY DIFFRACTION1allK1
11X-RAY DIFFRACTION1allL1
12X-RAY DIFFRACTION1allM1
13X-RAY DIFFRACTION1allN1
14X-RAY DIFFRACTION1allF1

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