[English] 日本語
Yorodumi
- PDB-3hl2: The crystal structure of the human SepSecS-tRNASec complex -

+
Open data


ID or keywords:

Loading...

-
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-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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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).

-
Components

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more