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- PDB-4zdp: The crystal structure of Y334C mutant of human SepSecS in complex... -

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Basic information

Entry
Database: PDB / ID: 4zdp
TitleThe crystal structure of Y334C mutant of human SepSecS in complex with selenocysteine tRNA (tRNASec)
Components
  • O-phosphoseryl-tRNA(Sec) selenium transferase
  • selenocysteine tRNA
KeywordsTransferase/RNA / selenocysteine / tRNA / mutation / pyridoxal phosphate / Transferase-RNA complex
Function / homology
Function and homology information


O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase / O-phosphoseryl-tRNA(Sec) selenium transferase activity / conversion of seryl-tRNAsec to selenocys-tRNAsec / selenocysteine incorporation / Selenocysteine synthesis / tRNA binding / nucleus / cytoplasm / cytosol
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 / PHOSPHATE ION / : / RNA / RNA (> 10) / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsFrench, 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: Sci Rep / Year: 2016
Title: Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase.
Authors: Puppala, A.K. / French, R.L. / Matthies, D. / Baxa, U. / Subramaniam, S. / Simonovic, M.
History
DepositionApr 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: selenocysteine tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,24613
Polymers250,9335
Non-polymers1,3138
Water9,656536
1
A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
E: selenocysteine tRNA
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)252,24613
Polymers250,9335
Non-polymers1,3138
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+y+2,y,-z+1/31
2
C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
E: selenocysteine tRNA
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)252,24613
Polymers250,9335
Non-polymers1,3138
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+2/31
Unit cell
Length a, b, c (Å)167.263, 167.263, 240.146
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-1139-

HOH

21B-1170-

HOH

31B-1197-

HOH

41C-1175-

HOH

51D-1202-

HOH

Detailssymmetry operation on chains A, B and conformer A of chain E: X, X-Y, -Z (0 -1 0); or on chains C and D and conformer B of chain E: -X+Y, Y, -Z+1/3 (0 0 0)

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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: 55741.180 Da / Num. of mol.: 4 / Mutation: Y334C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPSECS, TRNP48 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21
References: UniProt: Q9HD40, O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase
#2: RNA chain selenocysteine tRNA


Mass: 27968.516 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) / References: GenBank: 28372595
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.86 Å3/Da / Density % sol: 71.44 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na-cacodylate, pH 6.0 0.24M lithium citrate 8% (w/v) PEG 3,350
PH range: 6

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 98463 / % possible obs: 94 % / Redundancy: 6.1 % / Biso Wilson estimate: 49.26 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.051 / Rrim(I) all: 0.118 / Χ2: 1.118 / Net I/av σ(I): 12.898 / Net I/σ(I): 9.5 / Num. measured all: 599300
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.7-2.755.647270.6160.5061.18291.3
2.75-2.85.647140.6980.4291.14690.70.981
2.8-2.855.647100.7430.3691.15590.60.8470.928
2.85-2.915.647400.7880.3041.2910.6980.765
2.91-2.975.647150.860.2581.20590.40.5930.649
2.97-3.045.647680.8930.2151.173910.4950.542
3.04-3.125.747100.9280.1681.20790.80.3890.425
3.12-3.25.747490.9430.1411.19991.10.3270.358
3.2-3.35.747730.9580.1211.20291.70.280.306
3.3-3.45.847920.9710.11.19891.40.2320.254
3.4-3.524.947860.9410.1141.57591.90.2320.26
3.52-3.665.349030.970.0821.17194.10.1730.192
3.66-3.835.550100.9780.0641.1895.50.1380.153
3.83-4.035.246280.970.0581.14988.60.1170.132
4.03-4.296.852510.9950.0340.95799.90.0820.089
4.29-4.627.252420.9970.0280.961000.0690.075
4.62-5.087.552660.9980.0240.9121000.0620.066
5.08-5.817.652590.9980.0240.9931000.0620.066
5.81-7.327.553110.9990.021.00399.90.0510.055
7.32-50754090.9990.0131.06999.50.0310.034

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HL2

3hl2


Resolution: 2.703→41.649 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 5009 5.11 %
Rwork0.2001 93088 -
obs0.2018 98097 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 253.38 Å2 / Biso mean: 46.0277 Å2 / Biso min: 11.64 Å2
Refinement stepCycle: final / Resolution: 2.703→41.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13437 1585 80 536 15638
Biso mean--38.17 36.44 -
Num. residues----1848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01217402
X-RAY DIFFRACTIONf_angle_d1.05624283
X-RAY DIFFRACTIONf_chiral_restr0.0522910
X-RAY DIFFRACTIONf_plane_restr0.0062557
X-RAY DIFFRACTIONf_dihedral_angle_d14.0936833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.703-2.73370.35831460.27932771291784
2.7337-2.76580.28541440.26753023316791
2.7658-2.79960.32651520.26142998315091
2.7996-2.8350.32981350.26263014314990
2.835-2.87230.30091460.25323034318091
2.8723-2.91160.31451640.24752960312491
2.9116-2.95320.26971830.24342991317491
2.9532-2.99730.30141540.24272982313690
2.9973-3.04410.24781370.23363042317991
3.0441-3.0940.23961770.23172984316191
3.094-3.14730.2631780.23572982316091
3.1473-3.20450.28031550.24652993314891
3.2045-3.26610.29441550.23413057321292
3.2661-3.33280.27361850.23573021320691
3.3328-3.40520.2721610.23033044320592
3.4052-3.48440.30491560.25923012316890
3.4844-3.57150.23361540.20383106326094
3.5715-3.6680.24951820.21553066324893
3.668-3.77590.28851510.22113095324694
3.7759-3.89760.2241870.20613112329994
3.8976-4.03680.23561740.19682878305287
4.0368-4.19830.18911690.160233243493100
4.1983-4.38920.17751720.144133483520100
4.3892-4.62030.20641960.151232963492100
4.6203-4.90940.18481680.143133413509100
4.9094-5.28780.1671770.154933313508100
5.2878-5.81860.2211870.175333253512100
5.8186-6.65760.22771980.195433583556100
6.6576-8.37670.21381870.183933733560100
8.3767-41.65440.18341790.20373227340694

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