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- PDB-7y1h: Controlling fibrosis using compound with novel binding mode to pr... -

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Basic information

Entry
Database: PDB / ID: 7y1h
TitleControlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsTRANSLATION/INHIBITOR / prolyl-trna synthetase / inhibitor / fibrosis / binding mode / TRANSLATION / TRANSLATION-INHIBITOR complex
Function / homology
Function and homology information


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 / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation ...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 / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / GAIT complex / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to type II interferon / RNA stem-loop binding / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
C-terminal domain of ProRS / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / WHEP-TRS domain / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain ...C-terminal domain of ProRS / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / WHEP-TRS domain / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / 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 / Translation Initiation Factor IF3 / Anticodon-binding 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 / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-F99 / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsKim, S. / Yoon, I. / Son, J. / Park, S. / Hwang, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Embo Mol Med / Year: 2023
Title: Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1.
Authors: Yoon, I. / Kim, S. / Cho, M. / You, K.A. / Son, J. / Lee, C. / Suh, J.H. / Bae, D.J. / Kim, J.M. / Oh, S. / Park, S. / Kim, S. / Cho, S.H. / Park, S. / Bang, K. / Seo, M. / Kim, J.H. / Lee, ...Authors: Yoon, I. / Kim, S. / Cho, M. / You, K.A. / Son, J. / Lee, C. / Suh, J.H. / Bae, D.J. / Kim, J.M. / Oh, S. / Park, S. / Kim, S. / Cho, S.H. / Park, S. / Bang, K. / Seo, M. / Kim, J.H. / Lee, B. / Park, J.S. / Hwang, K.Y. / Kim, S.
History
DepositionJun 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional glutamate/proline--tRNA ligase
B: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,06112
Polymers116,1752
Non-polymers1,88610
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-101 kcal/mol
Surface area38300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.698, 92.364, 87.504
Angle α, β, γ (deg.)90.000, 108.200, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 2 molecules AB

#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


Mass: 58087.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli)
References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase

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Non-polymers , 5 types, 211 molecules

#2: Chemical ChemComp-F99 / 1-(5-chloranyl-4-methyl-benzimidazol-1-yl)-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one


Mass: 321.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: polyethylene glycol 3350, CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→37.9 Å / Num. obs: 65979 / % possible obs: 89.02 % / Redundancy: 4.1 % / Biso Wilson estimate: 30.37 Å2 / Rpim(I) all: 0.028 / Net I/σ(I): 23.384
Reflection shellResolution: 1.99→2.02 Å / Num. unique obs: 2313 / CC1/2: 0.613 / Rpim(I) all: 0.201 / % possible all: 63.2

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Processing

Software
NameVersionClassification
PHENIX1.20_4438refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K86

4k86


Resolution: 1.99→37.9 Å / SU ML: 0.3102 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 27.3166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 1998 3.03 %
Rwork0.207 63981 -
obs0.208 65979 89.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.34 Å2
Refinement stepCycle: LAST / Resolution: 1.99→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7698 0 112 201 8011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00757994
X-RAY DIFFRACTIONf_angle_d1.096910842
X-RAY DIFFRACTIONf_chiral_restr0.06171175
X-RAY DIFFRACTIONf_plane_restr0.00841401
X-RAY DIFFRACTIONf_dihedral_angle_d6.59831080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.37691040.37993328X-RAY DIFFRACTION65.48
2.04-2.10.38351270.34984051X-RAY DIFFRACTION78.83
2.1-2.160.34671260.32744069X-RAY DIFFRACTION80.1
2.16-2.230.33561340.29754253X-RAY DIFFRACTION82.99
2.23-2.310.31351370.27034379X-RAY DIFFRACTION85.13
2.31-2.40.2911370.264403X-RAY DIFFRACTION86.53
2.4-2.510.25541440.24224586X-RAY DIFFRACTION89.67
2.51-2.640.31531460.22854721X-RAY DIFFRACTION91.76
2.64-2.810.30331520.20524848X-RAY DIFFRACTION94.97
2.81-3.020.25031540.20384948X-RAY DIFFRACTION96.61
3.02-3.330.18551580.18875059X-RAY DIFFRACTION98.16
3.33-3.810.22021590.17135103X-RAY DIFFRACTION98.87
3.81-4.80.17931600.15335112X-RAY DIFFRACTION98.95
4.8-37.90.22031600.1895121X-RAY DIFFRACTION97.67

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