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- PDB-7yse: Crystal structure of E. coli heterotetrameric GlyRS in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7yse
TitleCrystal structure of E. coli heterotetrameric GlyRS in complex with tRNA
Components
  • (Glycine--tRNA ligase ...) x 2
  • RNA (76-MER)
KeywordsTRANSFERASE/RNA / aminoacyl-tRNA synthetase / hetertetramer / drug target / protein-tRNA complex / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


glycine-tRNA ligase complex / glycyl-tRNA aminoacylation / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / tRNA binding / ATP binding / cytosol
Similarity search - Function
Glycine-tRNA ligase, beta subunit / Glycyl-tRNA synthetase beta subunit / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / DALR anticodon binding / DALR anticodon binding domain / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
Chem-JPO / : / RNA / RNA (> 10) / Glycine--tRNA ligase alpha subunit / Glycine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.907 Å
AuthorsHan, L. / Ju, Y. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177140 China
CitationJournal: Sci Adv / Year: 2023
Title: The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements.
Authors: Han, L. / Luo, Z. / Ju, Y. / Chen, B. / Zou, T. / Wang, J. / Xu, J. / Gu, Q. / Yang, X.L. / Schimmel, P. / Zhou, H.
History
DepositionAug 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine--tRNA ligase alpha subunit
B: Glycine--tRNA ligase alpha subunit
C: Glycine--tRNA ligase beta subunit
D: Glycine--tRNA ligase beta subunit
E: RNA (76-MER)
F: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,55514
Polymers274,5336
Non-polymers1,0218
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23230 Å2
ΔGint-155 kcal/mol
Surface area89530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.710, 162.123, 324.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

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Glycine--tRNA ligase ... , 2 types, 4 molecules ABCD

#1: Protein Glycine--tRNA ligase alpha subunit / Glycyl-tRNA synthetase alpha subunit / GlyRS


Mass: 34806.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glyQ, glyS(A), b3560, JW3531 / Production host: Escherichia coli (E. coli) / References: UniProt: P00960, glycine-tRNA ligase
#2: Protein Glycine--tRNA ligase beta subunit / Glycyl-tRNA synthetase beta subunit / GlyRS


Mass: 77981.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glyS, glyS(B), b3559, JW3530 / Production host: Escherichia coli (E. coli) / References: UniProt: P00961, glycine-tRNA ligase

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RNA chain , 1 types, 2 molecules EF

#3: RNA chain RNA (76-MER)


Mass: 24478.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1609454293

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Non-polymers , 3 types, 22 molecules

#4: Chemical ChemComp-JPO / [(2R,3S,4R,5R)-5-(6-azanyl-2-chloranyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-(2-azanylethanoyl)sulfamate


Mass: 437.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16ClN7O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.15M MgCl2, 0.1M NaCl, 0.1M Tris-HCl pH 8.5, 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.907→162.12 Å / Num. obs: 85473 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.059 / Net I/σ(I): 9.4
Reflection shellResolution: 2.907→3.06 Å / Rmerge(I) obs: 0.749 / Num. unique obs: 12313 / CC1/2: 0.774 / Rpim(I) all: 0.304

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7eiv, 4mgm

7eiv

4mgm


Resolution: 2.907→50.005 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.898 / SU B: 40.39 / SU ML: 0.332 / Cross valid method: FREE R-VALUE / ESU R: 0.834 / ESU R Free: 0.356
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2598 4393 5.145 %
Rwork0.2296 80999 -
all0.231 --
obs-85392 99.885 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 77.244 Å2
Baniso -1Baniso -2Baniso -3
1-6.585 Å20 Å20 Å2
2---2.903 Å20 Å2
3----3.682 Å2
Refinement stepCycle: LAST / Resolution: 2.907→50.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14340 2952 62 14 17368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01217984
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714689
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.57125139
X-RAY DIFFRACTIONr_angle_other_deg1.1711.71334028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55651875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03722.309771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.983152280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.00415102
X-RAY DIFFRACTIONr_chiral_restr0.0510.22523
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023838
X-RAY DIFFRACTIONr_nbd_refined0.1840.23535
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.214484
X-RAY DIFFRACTIONr_nbtor_refined0.170.28116
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.27287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2386
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0590.21
X-RAY DIFFRACTIONr_nbd_other0.1730.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.21
X-RAY DIFFRACTIONr_mcbond_it2.0735.9847520
X-RAY DIFFRACTIONr_mcbond_other2.0735.9837517
X-RAY DIFFRACTIONr_mcangle_it3.4748.9759389
X-RAY DIFFRACTIONr_mcangle_other3.4758.9759388
X-RAY DIFFRACTIONr_scbond_it2.0686.37710463
X-RAY DIFFRACTIONr_scbond_other2.0686.37710464
X-RAY DIFFRACTIONr_scangle_it3.4949.57215750
X-RAY DIFFRACTIONr_scangle_other3.4939.57215751
X-RAY DIFFRACTIONr_lrange_it5.74570.51720105
X-RAY DIFFRACTIONr_lrange_other5.74570.51920106
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.907-2.9820.3312980.32858900.32861880.7920.781000.319
2.982-3.0640.3333250.30157560.30360810.8220.8251000.289
3.064-3.1520.3342810.29256250.29459060.8330.8431000.277
3.152-3.2490.2953170.27953870.2857040.8350.8581000.261
3.249-3.3550.32850.27452910.27555770.8640.8799.98210.259
3.355-3.4720.2822920.25351070.25453990.8720.8861000.238
3.472-3.6020.2792720.24149100.24351850.8870.90499.94210.229
3.602-3.7490.2392500.22547540.22550060.9150.91999.960.216
3.749-3.9140.2512660.21645470.21848210.9110.92699.83410.212
3.914-4.1040.242310.21144110.21246450.9140.92999.93540.21
4.104-4.3250.2542250.20241730.20544010.9170.92999.93180.207
4.325-4.5850.2621920.18739870.1941810.9120.94299.95220.199
4.585-4.8980.2051820.18537590.18639440.9430.94899.92390.2
4.898-5.2870.2272090.19734810.19936930.9280.93999.91880.215
5.287-5.7850.2631650.22232200.22433930.920.92599.76420.239
5.785-6.4570.2421790.2529160.24930990.9150.91899.87090.27
6.457-7.4350.2621510.22826330.2327860.9270.92899.92820.261
7.435-9.0560.2241040.20322740.20423860.9380.94399.66470.241
9.056-12.6020.2211020.217770.20118790.9490.9541000.237
12.602-50.0050.328670.32511010.32511840.8750.87998.64870.47
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)
10.2553-0.10550.02160.4839-0.07680.5493-0.02130.01760.0226-0.0052-0.03860.02380.19030.00420.05990.0885-0.03650.07490.29060.01950.2383-23.1766-39.299-28.2005
20.25990.1697-0.12720.8499-0.69150.6207-0.03340.00160.0084-0.17160.07510.0080.2246-0.0487-0.04170.2282-0.040.05030.2113-0.03180.1856-26.0945-63.132-29.5822
30.0597-0.0045-0.15150.1921-0.13780.50420.01930.00090.02080.0104-0.0534-0.0794-0.05160.03490.03410.0207-0.04140.04640.36050.03330.2562-13.4649-7.7551-37.4691
40.0511-0.1163-0.07430.55010.13940.1561-0.049-0.04150.0009-0.27770.0884-0.02140.1679-0.0003-0.03940.6864-0.10850.03910.1652-0.01450.0987-25.0886-94.2443-42.0013
50.4607-0.0835-0.45370.03060.05870.48330.140.17120.0216-0.0058-0.010.0685-0.1666-0.1836-0.13010.06830.0540.09870.50510.10830.3439-35.38150.9152-51.2993
60.8993-0.44710.04611.02320.19670.2321-0.0431-0.0830.183-0.0334-0.0641-0.28650.368-0.02140.10720.92660.14590.3540.27930.02990.2563-1.514-100.1694-33.239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA3 - 300
2X-RAY DIFFRACTION2ALLB2 - 300
3X-RAY DIFFRACTION3ALLC1 - 688
4X-RAY DIFFRACTION4ALLD3 - 688
5X-RAY DIFFRACTION5ALLE1 - 76
6X-RAY DIFFRACTION6ALLF1 - 76

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