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- PDB-9yon: Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA... -

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Basic information

Entry
Database: PDB / ID: 9yon
TitleCrystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69
ComponentsProline--tRNA ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


Ala-tRNA(Pro) deacylase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / ATP binding / cytoplasm
Similarity search - Function
YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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 ...YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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 / 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 II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
: / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69
Authors: Liu, L. / Lovell, S. / Seibold, S. / Battaile, K.P.
History
DepositionOct 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,04812
Polymers58,9861
Non-polymers1,06111
Water1448
1
A: Proline--tRNA ligase
hetero molecules

A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,09524
Polymers117,9732
Non-polymers2,12222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7610 Å2
ΔGint-206 kcal/mol
Surface area39140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.660, 106.660, 185.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Proline--tRNA ligase / Prolyl-tRNA synthetase / ProRS


Mass: 58986.496 Da / Num. of mol.: 1 / Fragment: UNP residues 249-746
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: proRS, PFL0670c / Plasmid: PlfaA.18681.a.B4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I5R7, proline-tRNA ligase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-A1CYM / N-[(3M)-3-(4-aminothieno[3,2-d]pyrimidin-6-yl)benzene-1-sulfonyl]-L-prolinamide


Mass: 403.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N5O3S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Grid Salt screen H8 : 4.0M NaCl, 0.1M Citric acid/citrate, pH 5.0. CrpaA.01302.a.B2.PW39348 at 21.9 mg/mL. 2mM inhibitor added to the protein prior to crystallization. plate 19968 H8 drop 1, ...Details: Grid Salt screen H8 : 4.0M NaCl, 0.1M Citric acid/citrate, pH 5.0. CrpaA.01302.a.B2.PW39348 at 21.9 mg/mL. 2mM inhibitor added to the protein prior to crystallization. plate 19968 H8 drop 1, Puck: PSL-1107, Cryo: 2.5M Lithium sulfate. The data were somewhat anisotropic which produced residual density (Fo-Fc) thoughout the polypeptide. The anisotropically truncated data from staraniso were used for refinement. The original and anisotropic truncated data were both deposited.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 7, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.43→46.37 Å / Num. obs: 35030 / % possible obs: 75.3 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.026 / Rrim(I) all: 0.115 / Net I/σ(I): 17.3
Reflection shellResolution: 2.434→2.654 Å / % possible obs: 16.8 % / Redundancy: 20.3 % / Rmerge(I) obs: 2.254 / Num. measured all: 35561 / Num. unique obs: 1751 / Rpim(I) all: 0.51 / Rrim(I) all: 2.311 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5723: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→46.23 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 1646 4.71 %
Rwork0.2013 --
obs0.2028 34979 75.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 57 8 4017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034104
X-RAY DIFFRACTIONf_angle_d0.5445582
X-RAY DIFFRACTIONf_dihedral_angle_d18.4381487
X-RAY DIFFRACTIONf_chiral_restr0.044603
X-RAY DIFFRACTIONf_plane_restr0.004707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.510.925120.4868257X-RAY DIFFRACTION7
2.51-2.590.4794280.4485600X-RAY DIFFRACTION16
2.59-2.680.4458490.37151196X-RAY DIFFRACTION33
2.68-2.790.3851970.33291934X-RAY DIFFRACTION53
2.79-2.910.35711700.32373264X-RAY DIFFRACTION90
2.91-3.070.36711490.32793686X-RAY DIFFRACTION100
3.07-3.260.29222120.28763647X-RAY DIFFRACTION100
3.26-3.510.25771900.21673663X-RAY DIFFRACTION100
3.51-3.860.24872190.20843659X-RAY DIFFRACTION100
3.86-4.420.1811800.15873726X-RAY DIFFRACTION100
4.42-5.570.18341690.15553766X-RAY DIFFRACTION100
5.57-46.230.20291710.17583935X-RAY DIFFRACTION100
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)
11.08280.0580.10051.32950.03452.213-0.19020.2913-0.32940.30950.12230.17780.2846-0.04480.09680.44420.1150.14440.2861-0.04460.4257-25.0461-45.86418.0548
21.3266-0.42110.03821.4444-0.45861.2174-0.03880.01080.05670.36550.0787-0.0704-0.23780.1016-0.04560.69170.18460.08560.3948-0.02150.3798-21.6942-33.61621.2405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 248 through 403 )
2X-RAY DIFFRACTION2chain 'A' and (resid 404 through 746 )

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