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- PDB-2azx: Charged and uncharged tRNAs adopt distinct conformations when com... -

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Basic information

Entry
Database: PDB / ID: 2azx
TitleCharged and uncharged tRNAs adopt distinct conformations when complexed with human tryptophanyl-tRNA synthetase
Components
  • 72-MER
  • Tryptophanyl-tRNA synthetase
KeywordsLigase/RNA / two synthetase-tRNA complex with distinct conformations / association complex and dissociation complex / Ligase-RNA COMPLEX
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / angiogenesis / translation ...tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / angiogenesis / translation / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / protein homodimerization activity / protein-containing complex / extracellular exosome / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) ...WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S15/NS1, RNA-binding / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHAN / RNA / RNA (> 10) / Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsYang, X.L. / Otero, F.J. / Ewalt, K.L. / Liu, J. / Swairjo, M.A. / Kohrer, C. / RajBhandary, U.L. / Skene, R.J. / McRee, D.E. / Schimmel, P.
CitationJournal: Embo J. / Year: 2006
Title: Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis.
Authors: Yang, X.L. / Otero, F.J. / Ewalt, K.L. / Liu, J. / Swairjo, M.A. / Kohrer, C. / RajBhandary, U.L. / Skene, R.J. / McRee, D.E. / Schimmel, P.
History
DepositionSep 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Remark 600HETEROGEN TRP 601 and 602 are associated with protein chain A TRP 603 is associated with protein chain B

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 72-MER
D: 72-MER
A: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,32620
Polymers157,5444
Non-polymers1,78216
Water39622
1
C: 72-MER
A: Tryptophanyl-tRNA synthetase
hetero molecules

C: 72-MER
A: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,12916
Polymers157,5444
Non-polymers1,58512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
2
D: 72-MER
B: Tryptophanyl-tRNA synthetase
hetero molecules

D: 72-MER
B: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,52224
Polymers157,5444
Non-polymers1,97820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Unit cell
Length a, b, c (Å)114.058, 132.621, 246.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-1004-

HOH

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Components

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RNA chain / Protein , 2 types, 4 molecules CDAB

#1: RNA chain 72-MER


Mass: 24180.357 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: In vitro transcription. The sequence of this tRNA naturally exists in Bos taurus (Bovine)
#2: Protein Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase / TrpRS / IFP53 / hWRS


Mass: 54591.629 Da / Num. of mol.: 2 / Mutation: S213G, Y214D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WARS, WRS / Plasmid: pBMS508 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23381, tryptophan-tRNA ligase

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Non-polymers , 5 types, 38 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.99 Å3/Da / Density % sol: 59 %
Description: THE STRUCTURE FACTOR FILE contains FRIEDEL PAIRS.
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: Ammonium sulfate, Hepes, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium sulfate11
2Hepes11
3H2O11
4Ammonium sulfate12
5H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9783 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2003
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 89701 / Num. obs: 87100 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.9
Reflection shellResolution: 2.8→2.9 Å / % possible all: 76.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3907 -Random
Rwork0.205 ---
all0.227 88967 --
obs0.211 79186 89 %-
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 3082 108 22 9445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2

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