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- PDB-7l1t: Crystal structure of human holo SepSecS -

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Basic information

Entry
Database: PDB / ID: 7l1t
TitleCrystal structure of human holo SepSecS
ComponentsO-phosphoseryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / selenocysteine synthesis / protein translation / PLP-dependent enzyme / RNA binding
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
O-phosphoseryl-tRNA(Sec) selenium transferase / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / Peroxidases heam-ligand binding site / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-PLR / PHOSPHATE ION / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsPuppala, A. / Castillo Suchkou, J. / Simonovic, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097042 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural basis for the tRNA-dependent activation of the terminal complex of selenocysteine synthesis in humans.
Authors: Puppala, A.K. / Castillo Suchkou, J. / French, R.L. / Kiernan, K.A. / Simonovic, M.
History
DepositionDec 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
A: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3013
Polymers57,9731
Non-polymers3282
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.216, 154.216, 76.257
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-1189-

HOH

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Components

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


Mass: 57972.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPSECS, TRNP48 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HD40, O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe first 20 amino acids correspond to the His-tag and its linker. Residue 1 of the protein begins ...The first 20 amino acids correspond to the His-tag and its linker. Residue 1 of the protein begins at residue 21 of the sequence.

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.36 M lithium citrate, 15% PEG 3,350, 0.1 M sodium cacodylic acid, 0.04 M HCl 4 mg/mL SepSecS, 1 mg/mL human tRNASec

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 25765 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.044 / Rrim(I) all: 0.099 / Χ2: 0.902 / Net I/σ(I): 4.5 / Num. measured all: 218393
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.25-2.298.912570.1690.912100
2.29-2.338.812690.2670.91999.8
2.33-2.388.812700.3040.8871000.899
2.38-2.428.612500.4470.9181000.78
2.42-2.488.512600.4740.9051000.684
2.48-2.538.212720.620.8991000.581
2.53-2.68.112630.6740.9271000.492
2.6-2.678.412690.7650.9211000.39
2.67-2.758.412740.8280.9271000.310.8890.946
2.75-2.838.912720.9040.9181000.240.7110.754
2.83-2.948.912800.9320.961000.180.5340.566
2.94-3.058.712780.9580.9811000.1260.3680.391
3.05-3.198.612820.97711000.090.2610.277
3.19-3.368.212820.9860.951000.0680.190.203
3.36-3.578.312980.9930.8971000.0460.1270.136
3.57-3.858.913000.9940.9031000.0330.0940.1
3.85-4.238.813050.9960.8591000.0260.0720.077
4.23-4.85813180.9960.8461000.0230.0610.065
4.85-6.18.213400.9970.80699.80.0220.0590.063
6.1-507.514260.9980.6998.30.0210.0540.058

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.79 Å30.64 Å
Translation6.79 Å30.64 Å

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Processing

Software
NameVersionClassificationNB
PHENIXdev_3951refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HL2

3hl2


Resolution: 2.25→30.64 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1999 7.76 %
Rwork0.1919 23759 -
obs0.1948 25758 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.82 Å2 / Biso mean: 65.4207 Å2 / Biso min: 32.17 Å2
Refinement stepCycle: final / Resolution: 2.25→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 20 96 3588
Biso mean--71.06 61.68 -
Num. residues----457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.310.3981390.38821643178298
2.31-2.370.36221390.335416501789100
2.37-2.440.37511400.315516681808100
2.44-2.520.33281410.305716701811100
2.52-2.610.35731410.277316781819100
2.61-2.710.321400.253616701810100
2.71-2.840.31431420.244816801822100
2.84-2.990.32711410.23316751816100
2.99-3.170.2891420.225716941836100
3.17-3.420.28291430.195816961839100
3.42-3.760.2191430.18117061849100
3.76-4.30.18741460.15817271873100
4.3-5.420.171460.149417481894100
5.42-30.640.17391560.15931854201099

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