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- PDB-4rqf: human Seryl-tRNA synthetase dimer complexed with one molecule of ... -

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Basic information

Entry
Database: PDB / ID: 4rqf
Titlehuman Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec
Components
  • Serine--tRNA ligase, cytoplasmic
  • selenocysteine tRNA
KeywordsLIGASE/RNA / aminoacyl-tRNA synthetase / classII aaRS / aminoacylation / serine / cytosol / LIGASE-RNA complex
Function / homology
Function and homology information


selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis ...selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis / cytoplasmic translation / tRNA binding / molecular adaptor activity / translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / 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) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / SERINE / RNA / RNA (> 10) / Serine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.503 Å
AuthorsXie, W. / Wang, C. / Guo, Y. / Tian, Q. / Jia, Q.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: SerRS-tRNASec complex structures reveal mechanism of the first step in selenocysteine biosynthesis.
Authors: Wang, C. / Guo, Y. / Tian, Q. / Jia, Q. / Gao, Y. / Zhang, Q. / Zhou, C. / Xie, W.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Derived calculations
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 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
C: selenocysteine tRNA
A: Serine--tRNA ligase, cytoplasmic
B: Serine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0407
Polymers148,8173
Non-polymers1,2234
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-45 kcal/mol
Surface area50920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.377, 108.894, 89.491
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: RNA chain selenocysteine tRNA


Mass: 28948.107 Da / Num. of mol.: 1 / Mutation: C2G, G70C / Source method: obtained synthetically / Details: in vitro synthesis / Source: (synth.) Homo sapiens (human)
#2: Protein Serine--tRNA ligase, cytoplasmic / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 59934.441 Da / Num. of mol.: 2 / Mutation: E447K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARS, SERS / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49591, serine-tRNA ligase
#3: 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
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3

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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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0., VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.503→50 Å / Num. all: 20009 / Num. obs: 19748 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Biso Wilson estimate: 115.87 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.4
Reflection shellResolution: 3.5→3.68 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.956 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L87, 3A3A

4l87

3a3a


Resolution: 3.503→37.625 Å / SU ML: 0.47 / σ(F): 1.37 / Phase error: 34.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.314 1008 5.11 %
Rwork0.2531 --
obs0.256 19707 96.93 %
all-19707 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.503→37.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7202 1341 76 0 8619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018918
X-RAY DIFFRACTIONf_angle_d1.23812381
X-RAY DIFFRACTIONf_dihedral_angle_d15.3773499
X-RAY DIFFRACTIONf_chiral_restr0.0731432
X-RAY DIFFRACTIONf_plane_restr0.0061363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.503-3.68770.35871410.30772313X-RAY DIFFRACTION86
3.6877-3.91850.33931350.28972727X-RAY DIFFRACTION100
3.9185-4.22070.32071490.26242703X-RAY DIFFRACTION100
4.2207-4.64470.3271770.25422684X-RAY DIFFRACTION100
4.6447-5.31520.28981310.24062744X-RAY DIFFRACTION100
5.3152-6.69050.34661540.26492764X-RAY DIFFRACTION99
6.6905-37.62710.27931210.23322764X-RAY DIFFRACTION94

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