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- PDB-8g9z: High-resolution crystal structure of the human selenomethionine-d... -

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Basic information

Entry
Database: PDB / ID: 8g9z
TitleHigh-resolution crystal structure of the human selenomethionine-derived SepSecS-tRNASec complex
Components
  • O-phosphoseryl-tRNA(Sec) selenium transferase
  • RNA (90-MER)
KeywordsTransferase/RNA / Selenocysteine synthesis / tRNA-binding / Protein biosynthesis / TRANSFERASE / 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 / 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 / : / RNA / RNA (> 10) / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsPuppala, A. / Simonovic, M. / Castillo Suchkou, J.
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
DepositionFeb 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)265,28013
Polymers263,8755
Non-polymers1,4058
Water23,9781331
1
A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
E: RNA (90-MER)
hetero molecules

A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
E: RNA (90-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,18814
Polymers292,7836
Non-polymers1,4058
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+2/31
Buried area30610 Å2
ΔGint-224 kcal/mol
Surface area85750 Å2
MethodPISA
2
C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
E: RNA (90-MER)
hetero molecules

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)294,18814
Polymers292,7836
Non-polymers1,4058
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+1/31
Buried area30230 Å2
ΔGint-220 kcal/mol
Surface area86630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.183, 167.183, 239.087
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
11A-1280-

HOH

21A-1314-

HOH

31B-1254-

HOH

41B-1325-

HOH

51C-1257-

HOH

61C-1301-

HOH

71D-1266-

HOH

81D-1317-

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: 58741.730 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.) Homo sapiens (human) / References: GenBank: 436409
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1331 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.66 Å3/Da / Density % sol: 66.35 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 5.0 mg/mL of human SeMet-SepSecS-tRNASec (with a 2-fold molar excess of SepSecS) was crystallized in in 0.28-0.3 M ammonium acetate, 19.8% (v/v) MPD, and 0.1 M sodium citrate titrated with 0. ...Details: 5.0 mg/mL of human SeMet-SepSecS-tRNASec (with a 2-fold molar excess of SepSecS) was crystallized in in 0.28-0.3 M ammonium acetate, 19.8% (v/v) MPD, and 0.1 M sodium citrate titrated with 0.057 M HCl to a pH of 5.5.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979439 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979439 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 456255 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.992 / Rrim(I) all: 0.266 / Χ2: 1.783 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starΧ2% possible all
2.07-2.1110.63.3981.07227110.3370.710.953100
2.11-2.1410.72.8711.33228960.4510.7890.956100
2.14-2.1910.72.5411.57227550.530.8330.954100
2.19-2.2310.72.1891.88228970.6470.8860.958100
2.23-2.2810.71.8432.2227570.7170.9140.973100
2.28-2.3310.71.5682.67227600.7880.9390.981100
2.33-2.3910.71.2533.4229410.8560.9611.001100
2.39-2.4510.61.0753.91228130.880.9681100
2.45-2.5310.60.8634.95227280.9240.981.034100
2.53-2.6110.60.6846.3228520.9490.9871.065100
2.61-2.710.40.5388.1228350.9690.9921.12100
2.7-2.819.50.42810.02228000.9750.9941.188100
2.81-2.949.20.30913.7228450.9850.9961.317100
2.94-3.0911.60.23421.51228170.9920.9981.504100
3.09-3.2911.60.18229.44227890.9950.9981.748100
3.29-3.5411.60.13842.96228130.9970.9992.111100
3.54-3.911.40.11254.94228290.9970.9992.521100
3.9-4.4611.20.09267.79227660.9980.9992.824100
4.46-5.629.50.08265.91228750.9980.9992.742100
5.62-5012.20.06785.39227760.99912.64799.6

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Processing

Software
NameVersionClassification
PHENIXDEV_3951refinement
HKL-2000data scaling
HKL-2000data reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→34.25 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 3974 0.87 %
Rwork0.177 --
obs0.177 456076 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14222 1820 92 1331 17465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219412
X-RAY DIFFRACTIONf_angle_d0.52827244
X-RAY DIFFRACTIONf_dihedral_angle_d13.8837966
X-RAY DIFFRACTIONf_chiral_restr0.0373240
X-RAY DIFFRACTIONf_plane_restr0.0052870
LS refinement shellResolution: 2.07→2.09 Å
RfactorNum. reflection% reflection
Rfree0.3959 206 -
Rwork0.357 15502 -
obs--97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.00610.61040.20581.703-0.14791.8570.05020.38220.3862-0.4937-0.03940.1993-0.3016-0.1988-0.01560.33520.104-0.01140.26180.01230.271611.72963.309663.4004
24.22552.240.29652.99340.00331.2185-0.0270.2919-0.1201-0.35320.0766-0.16860.0152-0.005-0.05510.19330.0631-0.00170.1502-0.03760.2119.0422-6.90869.7385
31.1250.17990.51540.74220.28041.32950.07870.01990.0145-0.02660.0502-0.2806-0.05550.2225-0.13350.2242-0.0405-0.00680.2674-0.08560.423140.4644-3.932984.4042
42.801-1.1292-0.45392.91670.9782.59620.0235-0.524-0.13420.37540.095-0.04520.2894-0.1013-0.09450.336-0.1083-0.11240.4398-0.0670.380537.4493-4.1081106.9461
54.0081-0.48510.70093.8585-2.0745.85160.0388-1.0057-0.20140.57550.10330.3767-0.0287-1.3708-0.25070.3751-0.1117-0.04040.7712-0.16620.52222.83324.0921109.9417
61.5992-0.50410.5253.2940.62031.6730.0072-0.5327-0.19540.30370.0640.11770.2223-0.00510.01220.20470.034-0.02810.41520.01420.2454-5.8345-1.120394.2483
71.4693-0.67180.14171.5346-0.17460.87150.0948-0.23340.37780.01970.0411-0.2239-0.14250.0407-0.12320.22210.01150.03560.257-0.12190.2863-16.220927.6286.7741
84.58110.789-0.57661.5863-0.21620.7950.12940.44290.7072-0.5278-0.0376-0.6056-0.09730.1448-0.07740.53370.00090.26710.3644-0.01430.733-2.687236.371769.1217
92.57720.5371-0.03781.83120.30571.53360.0339-0.43380.0870.37770.03520.0536-0.1718-0.0604-0.0250.29380.0537-0.01420.21140.00370.211976.980935.185953.6663
100.97420.18550.51410.8990.29421.36860.0482-0.021-0.24690.02560.08120.13130.1652-0.178-0.13070.2133-0.0408-0.07330.27020.03810.426266.735411.298435.1638
112.0994-0.42810.84223.7315-0.82032.6843-0.00350.4236-0.1007-0.5770.1042-0.03350.0180.2945-0.09070.3265-0.0924-0.11240.4421-0.06530.366968.341213.839812.4154
124.17590.1486-0.57184.54542.45555.2714-0.12820.80260.27-1.06330.4088-0.4287-1.18810.5912-0.31030.5908-0.2146-0.14090.55780.04370.536568.83330.75319.8462
132.3029-0.60210.74372.68660.42931.723-0.05570.348-0.0809-0.49790.1497-0.24590.0990.1893-0.01290.3873-0.0617-0.0010.2192-0.03720.248887.35852.877625.1839
141.1338-0.464-0.06821.89960.26530.9098-0.0410.0796-0.0362-0.15480.17480.4227-0.0261-0.1482-0.12540.259-0.0102-0.08460.21730.09480.282667.618176.111532.8089
152.68541.081-0.15942.7268-0.13240.5993-0.0822-0.4647-0.22750.58680.18660.89750.0725-0.1574-0.03580.42190.08180.13440.49690.24570.76753.239368.598550.5548
160.00780.0133-0.03740.0129-0.07370.4272-0.1650.252-0.35240.1497-0.404-0.2392-0.731-0.4556-0.41280.84350.03820.28670.87070.14581.205637.679231.204459.7536
170.18440.1314-0.39170.0876-0.23791.34570.35830.1638-0.25230.18990.2711-0.1605-0.3971-0.2576-0.64970.8506-0.02370.14740.84210.06311.297837.160532.145859.7898
181.09530.4842-0.7660.367-0.3631.87290.21750.12750.55150.21170.02750.2817-0.4547-0.3047-0.230.65040.07130.05470.53150.04710.707537.722931.141359.7725
191.54730.4373-1.69640.896-1.04252.2544-0.291-0.10190.4586-0.0363-0.2080.2195-0.1864-0.27130.41140.7542-0.1477-0.10440.838-0.07231.024245.914317.016559.769
208.80324.97835.41372.94983.02263.3382-0.00460.21740.44390.2413-0.31670.1167-0.3844-0.07930.33480.38590.00950.07070.38830.07820.462444.852418.855459.7766
213.82041.82160.96922.02560.61081.21510.2880.52310.27970.4835-0.23150.1273-0.1856-0.074-0.01660.59790.00420.24170.58420.15110.709341.758324.176359.7822
220.36450.3593-0.29020.3381-0.31841.15460.30080.1020.22580.2222-0.04190.1265-0.6169-0.3366-0.17971.01270.36320.38690.53580.21671.275330.836543.233459.8075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 11 THROUGH 75 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 76 THROUGH 129 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 130 THROUGH 359 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 360 THROUGH 435 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 436 THROUGH 491 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 11 THROUGH 129 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 130 THROUGH 359 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 360 THROUGH 466 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 11 THROUGH 129 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 130 THROUGH 359 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 360 THROUGH 435 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 436 THROUGH 492 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 11 THROUGH 129 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 130 THROUGH 359 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 360 THROUGH 467 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 1 THROUGH 19 )
17X-RAY DIFFRACTION17CHAIN 'E' AND (RESID 20 THROUGH 28 )
18X-RAY DIFFRACTION18CHAIN 'E' AND (RESID 29 THROUGH 47C)
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 47D THROUGH 48 )
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESID 50 THROUGH 54 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 55 THROUGH 68 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 69 THROUGH 75 )

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