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- PDB-3hl2: The crystal structure of the human SepSecS-tRNASec complex -

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Basic information

Entry
Database: PDB / ID: 3hl2
TitleThe crystal structure of the human SepSecS-tRNASec complex
Components
  • O-phosphoseryl-tRNA(Sec) selenium transferase
  • tRNASec
KeywordsTRANSFERASE / selenocysteine / tRNASec / SepSecS / protein-RNA complex / Alternative splicing / Cytoplasm / Protein biosynthesis / Pyridoxal phosphate / Selenium
Function / homology
Function and homology information


O-phosphoseryl-tRNA(Sec) selenium transferase activity / O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase / conversion of seryl-tRNAsec to selenocys-tRNAsec / selenocysteine incorporation / Selenocysteine synthesis / tRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #2160 / O-phosphoseryl-tRNA(Sec) selenium transferase / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / Peroxidases heam-ligand binding site / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain ...Arc Repressor Mutant, subunit A - #2160 / O-phosphoseryl-tRNA(Sec) selenium transferase / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / Peroxidases heam-ligand binding site / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-PLR / PHOSPHOSERINE / Monothiophosphate / RNA / RNA (> 10) / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsPalioura, S. / Steitz, T.A. / Soll, D. / Simonovic, M.
CitationJournal: Science / Year: 2009
Title: The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation.
Authors: Palioura, S. / Sherrer, R.L. / Steitz, T.A. / Soll, D. / Simonovic, M.
History
DepositionMay 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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_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_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: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
E: tRNASec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,12816
Polymers252,1135
Non-polymers2,01511
Water5,188288
1
A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules

A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
E: tRNASec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,24217
Polymers252,1135
Non-polymers2,12912
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation6_545x,x-y-1,-z1
identity operation1_555x,y,z1
2
C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules

C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
E: tRNASec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,01415
Polymers252,1135
Non-polymers1,90110
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation5_555-x+y,y,-z+1/31
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.818, 166.818, 236.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11D-537-

HOH

21D-540-

HOH

DetailsThe physiologically active tetrameric assembly can be reconstructed by applying the following symmetry operation onto the chains A and B, and the conformer A of the chain E: X, X-Y, -Z (0 -1 0). Similarly, the physiologic tetramer can be built by applying the symmetry operation onto the chains C and D, and the conformer B of the chain E: -X+Y, Y, -Z+1/3 (0 0 0).

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Components

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Protein / RNA chain , 2 types, 5 molecules ABCDE

#1: Protein
O-phosphoseryl-tRNA(Sec) selenium transferase / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase / Sep-tRNA:Sec-tRNA ...Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase / Sep-tRNA:Sec-tRNA synthase / SepSecS / UGA suppressor tRNA-associated protein / tRNA(Ser/Sec)-associated antigenic protein / Liver-pancreas antigen / LP / Soluble liver antigen / SLA / SLA/LP autoantigen / SLA-p35


Mass: 55801.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPSECS, TRNP48 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) cd+
References: UniProt: Q9HD40, L-seryl-tRNASec selenium transferase
#2: RNA chain tRNASec


Mass: 28908.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a

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Non-polymers , 4 types, 299 molecules

#3: Chemical
ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H12NO5P
#4: Chemical ChemComp-TS6 / Monothiophosphate / phosphorothioic O,O,S-acid / Thiophosphate


Mass: 114.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H3O3PS
#5: Chemical
ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE / Phosphoserine


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8NO6P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 3.77 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 285 K / pH: 6.5
Details: 0.3M tri-lithium citrate, 18% (w/v) PEG 3,350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2008
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 89375 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 65.3 Å2 / Rsym value: 0.17 / Net I/σ(I): 6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1 / Rsym value: 0.94 / % possible all: 94.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BC8

3bc8


Resolution: 2.81→37.95 Å / SU ML: 0.4 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1991 2.24 %
Rwork0.203 --
obs0.203 89031 97.1 %
all-89375 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.94 Å2 / ksol: 0.28 e/Å3
Refinement stepCycle: LAST / Resolution: 2.81→37.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13707 3492 141 288 17628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8082-2.87840.32731390.3285935X-RAY DIFFRACTION93
2.8784-2.95620.35681330.31185948X-RAY DIFFRACTION94
2.9562-3.04310.3351390.30176151X-RAY DIFFRACTION96
3.0431-3.14130.3171450.27186293X-RAY DIFFRACTION99
3.1413-3.25350.33951470.26226284X-RAY DIFFRACTION99
3.2535-3.38370.2991440.24786292X-RAY DIFFRACTION99
3.3837-3.53760.28311420.2126298X-RAY DIFFRACTION99
3.5376-3.7240.22381470.18416274X-RAY DIFFRACTION99
3.724-3.9570.22791420.16346338X-RAY DIFFRACTION99
3.957-4.26220.1931430.14396268X-RAY DIFFRACTION98
4.2622-4.69040.18751390.1366292X-RAY DIFFRACTION98
4.6904-5.36750.17271420.14076251X-RAY DIFFRACTION97
5.3675-6.75620.19361440.1776233X-RAY DIFFRACTION96
6.7562-37.94950.18511450.19056183X-RAY DIFFRACTION94

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