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- PDB-4qei: Two distinct conformational states of GlyRS captured in crystal l... -

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Basic information

Entry
Database: PDB / ID: 4qei
TitleTwo distinct conformational states of GlyRS captured in crystal lattice
Components
  • Glycine--tRNA ligase
  • tRNA-Gly-CCC-2-2
KeywordsLIGASE/RNA / aminoacyl-tRNA synthetase / glycylation / glycyl-tRNA synthetase / tRNA ligase / LIGASE-RNA complex
Function / homology
Function and homology information


mitochondrial glycyl-tRNA aminoacylation / ATP:ATP adenylyltransferase activity / glycine-tRNA ligase / glycine-tRNA ligase activity / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule ...mitochondrial glycyl-tRNA aminoacylation / ATP:ATP adenylyltransferase activity / glycine-tRNA ligase / glycine-tRNA ligase activity / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein dimerization activity / mitochondrial matrix / axon / mitochondrion / extracellular exosome / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) ...Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / 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 II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / S15/NS1, RNA-binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / RNA / RNA (> 10) / Glycine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.875 Å
AuthorsXie, W. / Qin, X. / Deng, X. / Zhang, Q. / Li, Q.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis
Authors: Deng, X. / Qin, X. / Chen, L. / Jia, Q. / Zhang, Y. / Zhang, Z. / Lei, D. / Ren, G. / Zhou, Z. / Wang, Z. / Li, Q. / Xie, W.
History
DepositionMay 16, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Glycine--tRNA ligase
C: tRNA-Gly-CCC-2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4313
Polymers94,0842
Non-polymers3471
Water59433
1
A: Glycine--tRNA ligase
C: tRNA-Gly-CCC-2-2
hetero molecules

A: Glycine--tRNA ligase
C: tRNA-Gly-CCC-2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,8626
Polymers188,1684
Non-polymers6942
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17280 Å2
ΔGint-92 kcal/mol
Surface area64900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.605, 88.446, 81.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glycine--tRNA ligase / Diadenosine tetraphosphate synthetase / AP-4-A synthetase / Glycyl-tRNA synthetase / GlyRS


Mass: 71757.727 Da / Num. of mol.: 1 / Fragment: UNP residues 118-739 / Mutation: E71G, C157R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 293T / Gene: GARS / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41250, glycine-tRNA ligase
#2: RNA chain tRNA-Gly-CCC-2-2


Mass: 22326.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the RNA is obtained from in vitro transcription / Source: (synth.) Homo sapiens (human) / References: GenBank: 634721920
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 27% PEG600, 0.1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.875→50 Å / Num. all: 22411 / Num. obs: 22329 / % possible obs: 99.7 % / Observed criterion σ(I): 5.5 / Redundancy: 5.8 % / Biso Wilson estimate: 69.3 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 13.8
Reflection shellResolution: 2.875→3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2205 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KR3

4kr3


Resolution: 2.875→36.9 Å / FOM work R set: 0.7801 / SU ML: 0.33 / σ(F): 0 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 1132 5.08 %random
Rwork0.2135 ---
obs0.216 22270 98.04 %-
all-22411 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.54 Å2 / Biso mean: 63.52 Å2 / Biso min: 25 Å2
Refinement stepCycle: LAST / Resolution: 2.875→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 1476 23 33 5764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115992
X-RAY DIFFRACTIONf_angle_d1.7328464
X-RAY DIFFRACTIONf_chiral_restr0.0721003
X-RAY DIFFRACTIONf_plane_restr0.012839
X-RAY DIFFRACTIONf_dihedral_angle_d17.0772384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8748-3.00550.31671230.2412323244687
3.0055-3.16390.30691450.228826332778100
3.1639-3.3620.30981380.225626422780100
3.362-3.62140.28241580.215226322790100
3.6214-3.98540.25271440.206326732817100
3.9854-4.56120.20561420.19226852827100
4.5612-5.74320.28021490.203327082857100
5.7432-36.90350.26911330.22832842297599

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