[English] 日本語
Yorodumi
- PDB-7oe1: 30S ribosomal subunit from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oe1
Title30S ribosomal subunit from E. coli
Components
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
KeywordsRIBOSOME / 30S subunit / RNA
Function / homology
Function and homology information


mRNA 5'-UTR binding / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome ...mRNA 5'-UTR binding / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S2 signature 2. / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S17 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S21 / 30S ribosomal protein S2 / 30S ribosomal protein S14 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S17 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S21 / 30S ribosomal protein S2 / 30S ribosomal protein S14 / 30S ribosomal protein S11 / 30S ribosomal protein S9 / 30S ribosomal protein S18 / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 30S ribosomal protein S10 / 30S ribosomal protein S16 / 30S ribosomal protein S3 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS7 / 30S ribosomal protein S19 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli str. K-12 substr. MG1655 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsMaksimova, E. / Korepanov, A. / Baymukhametov, T. / Kravchenko, O. / Stolboushkina, E.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2021
Title: RbfA Is Involved in Two Important Stages of 30S Subunit Assembly: Formation of the Central Pseudoknot and Docking of Helix 44 to the Decoding Center.
Authors: Elena M Maksimova / Alexey P Korepanov / Olesya V Kravchenko / Timur N Baymukhametov / Alexander G Myasnikov / Konstantin S Vassilenko / Zhanna A Afonina / Elena A Stolboushkina /
Abstract: Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount ...Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount of data collected, the exact role of most assembly factors and mechanistic details of their operation remain unclear, mainly due to the shortage of high-resolution structural information. Here, using cryo-electron microscopy, we characterized 30S ribosomal particles isolated from an   strain with a deleted gene for the RbfA factor. The cryo-EM maps for pre-30S subunits were divided into six classes corresponding to consecutive assembly intermediates: from the particles with a completely unresolved head domain and unfolded central pseudoknot to almost mature 30S subunits with well-resolved body, platform, and head domains and partially distorted helix 44. The structures of two predominant 30S intermediates belonging to most populated classes obtained at 2.7 Å resolutions indicate that RbfA acts at two distinctive 30S assembly stages: early formation of the central pseudoknot including folding of the head, and positioning of helix 44 in the decoding center at a later stage. Additionally, it was shown that the formation of the central pseudoknot may promote stabilization of the head domain, likely through the RbfA-dependent maturation of the neck helix 28. An update to the model of factor-dependent 30S maturation is proposed, suggesting that RfbA is involved in most of the subunit assembly process.
History
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12857
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S rRNA
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6, fully modified isoform
H: 30S ribosomal protein S8
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
T: 30S ribosomal protein S20
B: 30S ribosomal protein S2
U: 30S ribosomal protein S21
C: 30S ribosomal protein S3
G: 30S ribosomal protein S7
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
S: 30S ribosomal protein S19


Theoretical massNumber of molelcules
Total (without water)787,56921
Polymers787,56921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area83710 Å2
ΔGint-668 kcal/mol
Surface area272980 Å2
MethodPISA

-
Components

-
RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S rRNA


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)

-
30S ribosomal protein ... , 20 types, 20 molecules DEFHKLOPQRTBUCGIJMNS

#2: Protein 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XM56
#3: Protein 30S ribosomal protein S5


Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2YBZ5
#4: Protein 30S ribosomal protein S6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P02358
#5: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XYQ3
#6: Protein 30S ribosomal protein S11


Mass: 13739.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpsK, FAZ83_23205
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2X4T2
#7: Protein 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A4S5B3M5
#8: Protein 30S ribosomal protein S15


Mass: 10319.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: C3SSQ8
#9: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XXS6
#10: Protein 30S ribosomal protein S17


Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A4S5APA8
#11: Protein 30S ribosomal protein S18


Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XHZ3
#12: Protein 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A4S5B3X7
#13: Protein 30S ribosomal protein S2


Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2W584
#14: Protein 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A5F1E8X4
#15: Protein 30S ribosomal protein S3


Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XYP0
#16: Protein 30S ribosomal protein S7


Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: C4ZUJ6
#17: Protein 30S ribosomal protein S9


Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XBM7
#18: Protein 30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XQX6
#19: Protein 30S ribosomal protein S13


Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XQ78
#20: Protein 30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2WD65
#21: Protein 30S ribosomal protein S19


Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: E3PL00

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 30S ribosomal subunit from E.coli / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.85 MDa
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD
Image recordingElectron dose: 2 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.14model fitting
13PHENIX1.18.2.-3874model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169371 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 4V4Q / Initial refinement model-ID: 1 / PDB-ID: 4V4Q

4v4q

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1AA
2AB
3AC
4AE
5AF
6AH
7AI
8AJ
9AK
10AG
11AL
12AM
13AN
14AO
15AP
16AQ
17AR
18AT
19AU
20AD
21AS

+
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://pdbjlvh1.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