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- PDB-9udm: Cocrystal structure of human cytosolic phenylalanyl-tRNA syntheta... -

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Basic information

Entry
Database: PDB / ID: 9udm
TitleCocrystal structure of human cytosolic phenylalanyl-tRNA synthetase and an inhibitor in the presence of ATP
Components
  • Phenylalanine--tRNA ligase alpha subunit
  • Phenylalanine--tRNA ligase beta subunit
KeywordsLIGASE / TRNA ligase / Inhibitor / Complex
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / Cytosolic tRNA aminoacylation / protein heterotetramerization / tRNA binding / translation / magnesium ion binding / RNA binding ...phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / Cytosolic tRNA aminoacylation / protein heterotetramerization / tRNA binding / translation / magnesium ion binding / RNA binding / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
PheRS DNA binding domain 2 / PheRS, DNA binding domain 1 / PheRS, DNA binding domain 3 / PheRS DNA binding domain 1 / PheRS DNA binding domain 3 / PheRS DNA binding domain 2 / Phenylalanine--tRNA ligase beta subunit, B1 domain / Phe-tRNA synthetase beta subunit B1 domain / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit ...PheRS DNA binding domain 2 / PheRS, DNA binding domain 1 / PheRS, DNA binding domain 3 / PheRS DNA binding domain 1 / PheRS DNA binding domain 3 / PheRS DNA binding domain 2 / Phenylalanine--tRNA ligase beta subunit, B1 domain / Phe-tRNA synthetase beta subunit B1 domain / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / B3/4 domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Putative DNA-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) / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-LCF / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsQiao, H. / Hei, Z. / Fang, P.
Funding support1items
OrganizationGrant numberCountry
Other governmentShanghai Science and Technology Committee grant 22ZR1475000
CitationJournal: To Be Published
Title: Cocrystal structure of human cytosolic phenylalanyl-tRNA synthetase and an inhibitor
Authors: Qiao, H. / Hei, Z. / Fang, P.
History
DepositionApr 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0283
Polymers102,6482
Non-polymers3801
Water00
1
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules

A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,0566
Polymers205,2964
Non-polymers7602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area23290 Å2
ΔGint-144 kcal/mol
Surface area66230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.904, 107.904, 279.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phenylalanine--tRNA ligase alpha subunit / CML33 / Phenylalanyl-tRNA synthetase alpha subunit / PheRS


Mass: 36433.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FARSA, FARS, FARSL, FARSLA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y285, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 66214.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FARSB, FARSLB, FRSB, HSPC173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSD9, phenylalanine-tRNA ligase
#3: Chemical ChemComp-LCF / [6-(4-CHLOROPHENYL)-2,2-DIMETHYL-7-PHENYL-2,3-DIHYDRO-1H-PYRROLIZIN-5-YL]ACETIC ACID / LICOFELONE


Mass: 379.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22ClNO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, inhibitor*YM
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

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.2 M sodium formate, 0.05 M tris pH 8.5, 8% v/v PEG 500 MME and 8% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.33→48.26 Å / Num. obs: 25133 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.055 / Rrim(I) all: 0.149 / Χ2: 1 / Net I/σ(I): 13 / Num. measured all: 179381
Reflection shellResolution: 3.33→3.56 Å / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.89 / Num. measured all: 32375 / Num. unique obs: 4439 / CC1/2: 0.504 / Rpim(I) all: 0.747 / Rrim(I) all: 2.036 / Χ2: 1 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4G

3l4g


Resolution: 3.33→48.26 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2557 1998 7.98 %
Rwork0.2193 --
obs0.2222 25043 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.33→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6809 0 27 0 6836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.415
X-RAY DIFFRACTIONf_dihedral_angle_d7.416965
X-RAY DIFFRACTIONf_chiral_restr0.0781097
X-RAY DIFFRACTIONf_plane_restr0.021247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.33-3.410.42781390.3661610X-RAY DIFFRACTION100
3.41-3.510.43881410.37031617X-RAY DIFFRACTION100
3.51-3.610.32111390.33391605X-RAY DIFFRACTION100
3.61-3.730.39151410.29181627X-RAY DIFFRACTION100
3.73-3.860.32051400.2761609X-RAY DIFFRACTION100
3.86-4.010.30471410.24971633X-RAY DIFFRACTION100
4.01-4.20.26891410.23661620X-RAY DIFFRACTION100
4.2-4.420.23151410.18781620X-RAY DIFFRACTION100
4.42-4.690.20061420.18291648X-RAY DIFFRACTION100
4.69-5.050.23921420.18441634X-RAY DIFFRACTION100
5.05-5.560.20871440.20161655X-RAY DIFFRACTION100
5.56-6.360.29941460.23351687X-RAY DIFFRACTION100
6.37-8.010.25961470.21511696X-RAY DIFFRACTION100
8.01-48.260.19651540.17861784X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 34.0935 Å / Origin y: -40.4696 Å / Origin z: 18.6453 Å
111213212223313233
T0.9507 Å2-0.039 Å2-0.0168 Å2-1.0177 Å2-0.1787 Å2--0.9299 Å2
L1.5548 °2-0.2577 °2-1.2251 °2-0.2909 °20.1261 °2--0.9171 °2
S-0.1287 Å °0.1852 Å °-0.2058 Å °-0.0474 Å °-0.0518 Å °0.062 Å °0.111 Å °-0.2066 Å °0.173 Å °
Refinement TLS groupSelection details: all

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