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- PDB-4hvc: Crystal structure of human prolyl-tRNA synthetase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4hvc
TitleCrystal structure of human prolyl-tRNA synthetase in complex with halofuginone and ATP analogue
ComponentsBifunctional glutamate/proline--tRNA ligase
Keywordsligase/ligase inhibitor / ligase / ligase-ligase 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 / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / RNA stem-loop binding / GAIT complex / cellular response to type II interferon / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain ...C-terminal domain of ProRS / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-HFG / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, H. / Sun, L. / Yang, X.L. / Schimmel, P.
CitationJournal: Nature / Year: 2012
Title: ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase.
Authors: Zhou, H. / Sun, L. / Yang, X.L. / Schimmel, P.
History
DepositionNov 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)120,14810
Polymers118,1272
Non-polymers2,0218
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-42 kcal/mol
Surface area38320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.544, 93.100, 87.004
Angle α, β, γ (deg.)90.00, 107.95, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Glutamate-- ...Bifunctional aminoacyl-tRNA synthetase / Cell proliferation-inducing gene 32 protein / Glutamate--tRNA ligase / Glutamyl-tRNA synthetase / GluRS / Proline--tRNA ligase / Prolyl-tRNA synthetase


Mass: 59063.453 Da / Num. of mol.: 2 / Fragment: ProRS part of EPRS (unp residues 1003-1513)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 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, 212 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-HFG / 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one / Halofuginone / Halofuginone


Mass: 414.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: alkaloid, medication*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.6 M CaCl2, 50 mM HEPES , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2012
RadiationMonochromator: Side scattering I-beam bent single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 73215
Reflection shellResolution: 2→2.03 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.43 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.888 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22725 3678 5 %RANDOM
Rwork0.20379 ---
obs0.20498 69440 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.541 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20.03 Å2
2--0.96 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7610 0 114 204 7928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227982
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.96510864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58824.095359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.044151325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021546
X-RAY DIFFRACTIONr_chiral_restr0.070.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216048
X-RAY DIFFRACTIONr_mcbond_it0.3441.54842
X-RAY DIFFRACTIONr_mcangle_it0.66927810
X-RAY DIFFRACTIONr_scbond_it1.13433140
X-RAY DIFFRACTIONr_scangle_it1.8624.53044
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 276 -
Rwork0.246 5060 -
obs--97.75 %
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)
12.6264-0.2175-2.20741.51730.96385.359-0.0363-0.35930.47540.30370.0296-0.1349-0.65070.39980.00660.2876-0.0278-0.14730.0938-0.06160.162720.381714.647638.5146
21.4281-0.10630.19540.9517-0.04931.4179-0.0205-0.08380.1080.0697-0.05590.2118-0.0755-0.21430.07640.00880.00710.01080.0393-0.03110.0629-0.99986.840323.1939
32.9-2.7211.18813.4979-1.21811.38040.0028-0.07970.02110.1443-0.057-0.30420.08750.03890.05420.2332-0.0077-0.04990.15690.03550.086426.9085-7.112248.9123
45.3652-4.35281.71845.499-1.32151.0708-0.1539-0.651-0.35680.59420.16340.3319-0.0369-0.2342-0.00940.2989-0.0140.06580.31770.05930.0579.6611-3.260953.5444
52.31591.25681.39353.11360.18162.5635-0.1939-0.23020.445-0.0134-0.02420.412-0.7017-0.31940.21820.51360.15260.05340.3721-0.18020.3794-10.329624.881844.3798
63.87140.04930.59832.7304-0.33431.5616-0.0474-0.44580.40060.30450.04510.5276-0.5068-0.56350.00230.35540.13450.10250.4176-0.16820.2651-12.701818.419742.7287
71.0324-0.1791-0.00071.93210.21770.99-0.0110.2180.0635-0.224-0.0664-0.1268-0.03680.10980.07740.03030.0040.01010.06550.02310.020715.29991.609510.7173
81.88250.4560.4241.47120.35011.4390.02540.2047-0.0623-0.05770.0041-0.22510.04980.2608-0.02960.01030.02110.01350.07190.00930.037626.4897-3.728814.4455
96.37221.33940.23642.369-0.5533.1620.3641-0.7183-0.57470.42-0.17620.6378-0.0284-0.5315-0.18790.2309-0.07860.07560.241-0.020.4006-5.9107-23.799814.3098
103.57970.9348-0.32351.226-0.17120.9143-0.06950.2782-0.3914-0.32150.01-0.22150.1880.1670.05950.24520.05830.00730.1633-0.11660.159623.8919-19.34730.1481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1016 - 1050
2X-RAY DIFFRACTION2A1051 - 1287
3X-RAY DIFFRACTION3A1288 - 1388
4X-RAY DIFFRACTION4A1389 - 1426
5X-RAY DIFFRACTION5A1427 - 1460
6X-RAY DIFFRACTION6A1461 - 1512
7X-RAY DIFFRACTION7B1015 - 1115
8X-RAY DIFFRACTION8B1116 - 1318
9X-RAY DIFFRACTION9B1319 - 1360
10X-RAY DIFFRACTION10B1361 - 1512

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