[English] 日本語
Yorodumi
- PDB-8uzw: Selenocysteine synthase- SelA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uzw
TitleSelenocysteine synthase- SelA
ComponentsL-seryl-tRNA(Sec) selenium transferase
KeywordsRNA BINDING PROTEIN / Selenocysteine / tRNASec / Sec-synthase
Function / homology
Function and homology information


L-seryl-tRNASec selenium transferase / L-seryl-tRNA(Sec) selenium transferase activity / selenocysteine incorporation / selenocysteine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
L-seryl-tRNA selenium transferase N-terminal domain / Selenocysteine synthase N terminal / L-seryl-tRNA(Sec) selenium transferase / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
L-seryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsBalasco Serrao, V.H. / Minari, K. / Pereira, H.M. / Thiemann, O.H.
Funding support Brazil, United States, 5items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)12/23730-1 Brazil
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U24GM129547 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10OD02509 United States
Brazilian National Council for Scientific and Technological Development (CNPq)232251/2014-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)140636/2013-7 Brazil
CitationJournal: Curr Res Struct Biol / Year: 2024
Title: Bacterial selenocysteine synthase structure revealed by single-particle cryoEM.
Authors: Vitor Hugo Balasco Serrão / Karine Minari / Humberto D'Muniz Pereira / Otavio Henrique Thiemann /
Abstract: The 21st amino acid, selenocysteine (Sec), is synthesized on its dedicated transfer RNA (tRNA). In bacteria, Sec is synthesized from Ser-tRNA by Selenocysteine Synthase (SelA), which is a pivotal ...The 21st amino acid, selenocysteine (Sec), is synthesized on its dedicated transfer RNA (tRNA). In bacteria, Sec is synthesized from Ser-tRNA by Selenocysteine Synthase (SelA), which is a pivotal enzyme in the biosynthesis of Sec. The structural characterization of bacterial SelA is of paramount importance to decipher its catalytic mechanism and its role in the regulation of the Sec-synthesis pathway. Here, we present a comprehensive single-particle cryo-electron microscopy (SPA cryoEM) structure of the bacterial SelA with an overall resolution of 2.69 Å. Using recombinant SelA, we purified and prepared samples for single-particle cryoEM. The structural insights from SelA, combined with previous and knowledge, underscore the indispensable role of decamerization in SelA's function. Moreover, our structural analysis corroborates previous results that show that SelA adopts a pentamer of dimers configuration, and the active site architecture, substrate binding pocket, and key K295 catalytic residue are identified and described in detail. The differences in protein architecture and substrate coordination between the bacterial enzyme and its counterparts offer compelling structural evidence supporting the independent molecular evolution of the bacterial and archaea/eukarya Ser-Sec biosynthesis present in the natural world.
History
DepositionNov 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Experimental preparation / Category: citation / em_sample_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_sample_support.grid_type
Revision 1.2May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-seryl-tRNA(Sec) selenium transferase
B: L-seryl-tRNA(Sec) selenium transferase
C: L-seryl-tRNA(Sec) selenium transferase
D: L-seryl-tRNA(Sec) selenium transferase
E: L-seryl-tRNA(Sec) selenium transferase
F: L-seryl-tRNA(Sec) selenium transferase
G: L-seryl-tRNA(Sec) selenium transferase
H: L-seryl-tRNA(Sec) selenium transferase
I: L-seryl-tRNA(Sec) selenium transferase
J: L-seryl-tRNA(Sec) selenium transferase


Theoretical massNumber of molelcules
Total (without water)508,95210
Polymers508,95210
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
L-seryl-tRNA(Sec) selenium transferase / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase


Mass: 50895.172 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: selA, fdhA, b3591, JW3564 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A821, L-seryl-tRNASec selenium transferase
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Bacterial Selenocysteine Synthase / Type: COMPLEX
Details: Heterologously expressed E. coli homodecameric Selenocysteine Synthase
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.51 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Details: 20 mM potassium phosphate pH 7.5, 100 mM sodium chloride, 2 mM 2-mercaptoethanol, and 10 uM pyridoxal 5-phosphate.
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMPotassium PhosphateKH2PO41
2100 mMSodium ChlorideNaClSodium chloride1
32 mM2-mercaptoethanol1
410 uMpyridoxal 5-phosphatePyridoxal phosphate1
SpecimenConc.: 3.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Monodisperse sample after size-exclusion chromatography
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: The sample was blotted for 2.5 seconds using a force of -10 and then swiftly plunged frozen into liquid ethane using the Vitrobot Mark IV - Thermo Fisher Scientific.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 45.4 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4592

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
4cryoSPARC4.2.1CTF correction
7Coot0.9.4model fitting
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 688602
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223410 / Symmetry type: POINT
Atomic model buildingB value: 95.2 / Protocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01128655
ELECTRON MICROSCOPYf_angle_d0.76738884
ELECTRON MICROSCOPYf_dihedral_angle_d6.5294089
ELECTRON MICROSCOPYf_chiral_restr0.0414651
ELECTRON MICROSCOPYf_plane_restr0.0065015

+
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