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- PDB-4ycu: Crystal structure of cladosporin in complex with human lysyl-tRNA... -

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Basic information

Entry
Database: PDB / ID: 4ycu
TitleCrystal structure of cladosporin in complex with human lysyl-tRNA synthetase
Components
  • Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
  • Lysine--tRNA ligase
Keywordsligase/ ligase inhibitor / Inhibitor / Complex / LysRS / cladosporin / ligase- ligase inhibitor complex
Function / homology
Function and homology information


ATP:ADP adenylyltransferase activity / type II pneumocyte differentiation / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / Selenoamino acid metabolism / diadenosine tetraphosphate biosynthetic process ...ATP:ADP adenylyltransferase activity / type II pneumocyte differentiation / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / Selenoamino acid metabolism / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / 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 / membrane / identical protein binding / 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
cladosporin / LYSINE / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Lysine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsFang, P. / Wang, J. / Guo, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100136 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106134 United States
CitationJournal: Chem. Biol. / Year: 2015
Title: Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.
Authors: Fang, P. / Han, H. / Wang, J. / Chen, K. / Chen, X. / Guo, M.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization

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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)124,63911
Polymers123,3923
Non-polymers1,2478
Water12,538696
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
C: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
hetero molecules

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)249,27922
Polymers246,7846
Non-polymers2,49516
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area27700 Å2
ΔGint-135 kcal/mol
Surface area77880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.194, 99.847, 268.987
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-990-

HOH

21B-1002-

HOH

31B-1032-

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, lysine-tRNA ligase
#2: Protein/peptide Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Multisynthase complex auxiliary component p38 / Protein JTV-1


Mass: 4911.680 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

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Non-polymers , 4 types, 704 molecules

#3: Chemical ChemComp-KRS / cladosporin / (3R)-3-[[(2R,6S)-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 292.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20O5
#4: Chemical ChemComp-LYS / LYSINE / Lysine


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 20000, Tris, sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 75891 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 26.57 Å2 / Rmerge(I) obs: 0.102 / Χ2: 0.954 / Net I/av σ(I): 19.692 / Net I/σ(I): 6 / Num. measured all: 561536
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.187.60.70974890.782100
2.18-2.267.30.55274780.87100
2.26-2.377.40.44475200.885100
2.37-2.497.60.3575620.879100
2.49-2.657.40.26675400.969100
2.65-2.857.50.18875390.972100
2.85-3.147.60.12276081.018100
3.14-3.597.40.08576011.235100
3.59-4.527.20.05176481.18599.7
4.52-507.10.03779060.75299.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 2.1→48.097 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 3602 5.01 %
Rwork0.1912 68353 -
obs0.1923 71955 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.12 Å2 / Biso mean: 31.6013 Å2 / Biso min: 15.23 Å2
Refinement stepCycle: final / Resolution: 2.1→48.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8239 0 86 699 9024
Biso mean--29.3 38.15 -
Num. residues----1035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068556
X-RAY DIFFRACTIONf_angle_d1.04511580
X-RAY DIFFRACTIONf_chiral_restr0.0511261
X-RAY DIFFRACTIONf_plane_restr0.0051498
X-RAY DIFFRACTIONf_dihedral_angle_d13.2223239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.17510.26472260.23354290451660
2.1751-2.26210.26443420.23796436677891
2.2621-2.36510.23593660.23177051741799
2.3651-2.48980.27293530.229672037556100
2.4898-2.64580.25314050.221971067511100
2.6458-2.850.23773930.214571457538100
2.85-3.13680.21143370.202672447581100
3.1368-3.59060.21313950.185971837578100
3.5906-4.52320.17884040.152472347638100
4.5232-48.10960.18313810.16967461784299
Refinement TLS params.Method: refined / Origin x: -3.0179 Å / Origin y: 6.9482 Å / Origin z: 30.5169 Å
111213212223313233
T0.1781 Å2-0.0576 Å2-0.0275 Å2-0.2117 Å20.0279 Å2--0.1712 Å2
L0.3215 °2-0.0571 °2-0.0228 °2-0.5497 °20.2454 °2--0.5444 °2
S-0.0076 Å °-0.0034 Å °0.0029 Å °0.0521 Å °0.0061 Å °-0.0298 Å °0.0994 Å °-0.0193 Å °0.0047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA72 - 700
2X-RAY DIFFRACTION1allA800
3X-RAY DIFFRACTION1allB72 - 700
4X-RAY DIFFRACTION1allB800
5X-RAY DIFFRACTION1allC2 - 32
6X-RAY DIFFRACTION1allH2 - 1542
7X-RAY DIFFRACTION1allI1 - 4

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