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- PDB-7mdl: High-resolution crystal structure of human SepSecS-tRNASec complex -

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Basic information

Entry
Database: PDB / ID: 7mdl
TitleHigh-resolution crystal structure of human SepSecS-tRNASec complex
Components
  • O-phosphoseryl-tRNA(Sec) selenium transferase
  • RNA (90-MER)
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 / cytoplasm / cytosol
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
CITRATE ANION / Chem-PLR / RNA / RNA (> 10) / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPuppala, A. / French, R.L. / 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
DepositionApr 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 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

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: RNA (90-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,37513
Polymers260,6865
Non-polymers1,6898
Water23,5821309
1
E: RNA (90-MER)

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,37513
Polymers260,6865
Non-polymers1,6898
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation6_566x,x-y+1,-z+11
2
E: RNA (90-MER)

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,37513
Polymers260,6865
Non-polymers1,6898
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation5_656-x+y+1,y,-z+4/31
Unit cell
Length a, b, c (Å)167.058, 167.058, 239.846
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-1197-

HOH

21A-1332-

HOH

31B-1222-

HOH

41B-1288-

HOH

51C-1171-

HOH

61C-1304-

HOH

71D-1225-

HOH

81D-1290-

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: 57944.504 Da / Num. of mol.: 4 / Mutation: V491A
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: RNA chain RNA (90-MER)


Mass: 28908.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.766.8
23.766.8
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2851vapor diffusion, sitting drop6.40.24 M lithium citrate, 10% PEG 3350 0.1 M, sodium cacodylate trihydrate, 2.0 mg/mL SepSecS mixed with 0.5 mg/mL tRNASec
2852vapor diffusion, sitting drop6.20.24 M lithium citrate, 9% PEG 3350, 0.1 M sodium cacodylate trihydrate, 6.0 mg/mL SepSecS mixed with 1.5 mg/mL tRNASec

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 165776 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.053 / Rrim(I) all: 0.144 / Χ2: 1.198 / Net I/σ(I): 7.9 / Num. measured all: 1176629
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.32-2.364.51.50181850.4030.7891.7040.9499.6
2.36-2.45.11.30382490.5010.6321.4530.94299.8
2.4-2.455.61.19482500.5620.5521.320.9599.9
2.45-2.561.00682290.6770.4451.1030.95399.9
2.5-2.556.60.87882300.7580.3660.9530.992100
2.55-2.616.90.76283000.8170.3110.8250.998100
2.61-2.686.90.63182280.8770.2580.6831.075100
2.68-2.7570.53382640.8990.2160.5761.069100
2.75-2.837.10.43682830.9290.1740.471.085100
2.83-2.927.20.34282630.9570.1360.3681.147100
2.92-3.037.40.27582600.970.1090.2961.23100
3.03-3.157.50.21583000.9810.0840.2311.371100
3.15-3.297.70.18182940.9870.0690.1941.306100
3.29-3.477.80.14582460.9910.0560.1561.342100
3.47-3.6880.11482890.9940.0430.1221.49100
3.68-3.978.10.08983450.9960.0340.0951.473100
3.97-4.378.20.07583010.9970.0280.081.33100
4.37-58.10.06683300.9970.0250.0711.34100
5-6.298.20.06584000.9970.0240.0691.249100
6.29-5080.05585300.9980.0210.0591.15599.6

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Processing

Software
NameVersionClassification
PHENIX3951refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HL2

3hl2


Resolution: 2.32→41.6 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 1945 1.18 %
Rwork0.176 162705 -
obs0.1763 164650 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.09 Å2 / Biso mean: 47.468 Å2 / Biso min: 18.06 Å2
Refinement stepCycle: final / Resolution: 2.32→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14141 1783 112 1311 17347
Biso mean--56.83 48.71 -
Num. residues----1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218682
X-RAY DIFFRACTIONf_angle_d0.61926110
X-RAY DIFFRACTIONf_chiral_restr0.0713115
X-RAY DIFFRACTIONf_plane_restr0.0052726
X-RAY DIFFRACTIONf_dihedral_angle_d12.0674074
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 (%)
2.32-2.380.32891040.2949114811158599
2.38-2.440.32841030.27061156111664100
2.44-2.510.29152080.24971150311711100
2.51-2.60.27661030.23591161711720100
2.6-2.690.26531060.21581163511741100
2.69-2.80.22362020.20281152911731100
2.8-2.920.2651020.18581164511747100
2.92-3.080.20572090.18371152811737100
3.08-3.270.18841030.16791164311746100
3.27-3.520.19161010.16341167611777100
3.52-3.880.18852080.15081160011808100
3.88-4.440.13921020.13251169511797100
4.44-5.590.15621960.1431168711883100
5.59-41.60.2056980.1753119051200399

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