[English] 日本語
Yorodumi
- PDB-6w6k: 30S-Activated-high-Mg2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w6k
Title30S-Activated-high-Mg2+
Components
  • (30S ribosomal protein ...) x 17
  • 16S rRNA
KeywordsRIBOSOME / 30S subunit / conformations / inactive / activated
Function / homology
Function and homology information


mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity, mRNA regulatory element binding ...mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity, mRNA regulatory element binding / endodeoxyribonuclease activity / positive regulation of RNA splicing / DNA-templated transcription, termination / maintenance of translational fidelity / positive regulation of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / cytosolic small ribosomal subunit / regulation of translation / regulation of mRNA stability / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / RNA binding / cytosol
Ribosomal protein S20 / Ribosomal protein S11, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast ...Ribosomal protein S20 / Ribosomal protein S11, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S13, bacterial-type / Ribosomal protein S10 domain / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, N-terminal / 30s ribosomal protein S13, C-terminal / Ribosomal protein S6 superfamily / Ribosomal protein S13-like, H2TH / Ribosomal protein S6 / Ribosomal protein S19 / Ribosomal protein S18 / Ribosomal protein S17 / Ribosomal protein S16 / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S13/S18 / Ribosomal protein S12/S23 / Ribosomal protein S11 / Ribosomal protein S10p/S20e / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal domain / S4 domain / Ribosomal protein S4/S9 N-terminal domain / KH domain / Ribosomal protein S3, C-terminal domain / Ribosomal protein S14/S29 / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein S10, conserved site / S15/NS1, RNA-binding / Ribosomal protein S11 / Ribosomal protein S17/S11 / Ribosomal protein S16 / Ribosomal protein S6 / Ribosomal protein S15 / Ribosomal protein S8 / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein S14 / Ribosomal protein S3, C-terminal / K homology domain superfamily, prokaryotic type / Ribosomal protein S10 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S18 / Ribosomal protein S19/S15 / Ribosomal protein S12, bacterial-type / Ribosomal protein S12/S23 / Ribosomal protein S20 / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain
30S ribosomal protein S3 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S18 / 30S ribosomal protein S16 / 30S ribosomal protein S4 / 30S ribosomal protein S19 / 30S ribosomal protein S20 ...30S ribosomal protein S3 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S18 / 30S ribosomal protein S16 / 30S ribosomal protein S4 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 30S ribosomal protein S6 / gb:1789840096: / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S15
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJahagirdar, D. / Jha, V. / Basu, B. / Gomez-Blanco, J. / Vargas, J. / Ortega, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)CIHR PJT- 153044 Canada
CitationJournal: RNA / Year: 2020
Title: Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy.
Authors: Dushyant Jahagirdar / Vikash Jha / Kaustuv Basu / Josue Gomez-Blanco / Javier Vargas / Joaquin Ortega /
Abstract: It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits ...It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an "active" and "inactive" conformation. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains unsolved. Here we used cryo-electron microscopy to obtain the structure of the inactive conformation of the 30S subunit to 3.6 Å resolution and study its motions. In the inactive conformation, an alternative base-pairing of three nucleotides causes the region of helix 44, forming the decoding center to adopt an unlatched conformation and the 3' end of the 16S rRNA positions similarly to the mRNA during translation. Incubation of inactive 30S subunits at 42°C reverts these structural changes. The air-water interface to which ribosome subunits are exposed during sample preparation also peel off some ribosomal proteins. Extended exposures to low magnesium concentrations make the ribosomal particles more susceptible to the air-water interface causing the unfolding of large rRNA structural domains. Overall, this study provides new insights about the conformational space explored by the 30S ribosomal subunit when the ribosomal particles are free in solution.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21558
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S rRNA
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)734,20119
Polymers734,17618
Non-polymers241
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
30S ribosomal protein ... , 17 types, 17 molecules CDEFHIJKLMNOPQRST

#2: Protein 30S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V3
#3: Protein 30S ribosomal protein S4 / / Small ribosomal subunit protein uS4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V8
#4: Protein 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7W1
#5: Protein 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02358
#6: Protein 30S ribosomal protein S8 / / Small ribosomal subunit protein uS8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7W7
#7: Protein 30S ribosomal protein S9 / / Small ribosomal subunit protein uS9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7X3
#8: Protein 30S ribosomal protein S10 / / Small ribosomal subunit protein uS10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R5
#9: Protein 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R9
#10: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7S3
#11: Protein 30S ribosomal protein S13 / / Small ribosomal subunit protein uS13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7S9
#12: Protein 30S ribosomal protein S14 / / Small ribosomal subunit protein uS14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG59
#13: Protein 30S ribosomal protein S15 /


Mass: 10319.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: A0A4S5B232, UniProt: P0ADZ4*PLUS
#14: Protein 30S ribosomal protein S16 / / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7T3
#15: Protein 30S ribosomal protein S17 / / Small ribosomal subunit protein uS17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG63
#16: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7T7
#17: Protein 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7U3
#18: Protein 30S ribosomal protein S20 / / Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7U7

-
RNA chain / Non-polymers , 2 types, 2 molecules A

#19: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#1: RNA chain 16S rRNA


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1789840096

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 30S-Activated-high-Mg2+ / Type: RIBOSOME / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/2
VitrificationCryogen name: ETHANE

-
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
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
7UCSF Chimeramodel fitting
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 407623 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 4V4Q

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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