[English] 日本語
Yorodumi
- PDB-9cl9: WT 12C IM fraction, B-b3 with RluB bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cl9
TitleWT 12C IM fraction, B-b3 with RluB bound
Components
  • (Large ribosomal subunit protein ...) x 10
  • 23S rRNA
  • Ribosomal large subunit pseudouridine synthase B
KeywordsRIBOSOME / 50S subunit / assembly intermediate / RNA-protein complex
Function / homology
Function and homology information


23S rRNA pseudouridine2605 synthase / 23S rRNA pseudouridine(2605) synthase activity / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / mRNA regulatory element binding translation repressor activity ...23S rRNA pseudouridine2605 synthase / 23S rRNA pseudouridine(2605) synthase activity / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / DNA-templated transcription termination / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Pseudouridine synthase, RsuA/RluB/E/F / Pseudouridine synthase, RsuA/RluB/E/F, conserved site / : / Rsu family of pseudouridine synthase signature. / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase, catalytic domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : ...Pseudouridine synthase, RsuA/RluB/E/F / Pseudouridine synthase, RsuA/RluB/E/F, conserved site / : / Rsu family of pseudouridine synthase signature. / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase, catalytic domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / : / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / : / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL23 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL21 / Ribosomal large subunit pseudouridine synthase B / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.04 Å
AuthorsLee, J. / Sheng, K. / Williamson, J.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136412 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053757 United States
CitationJournal: To Be Published
Title: 50S ribosome assembly intermediates at low temperature reveal bound RluB
Authors: Lee, J. / Sheng, K. / Williamson, J.R. / Gebert, L.
History
DepositionJul 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Q: Large ribosomal subunit protein bL20
R: Large ribosomal subunit protein bL21
T: Large ribosomal subunit protein uL23
2: Large ribosomal subunit protein bL34
A: Ribosomal large subunit pseudouridine synthase B
CA: 23S rRNA
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
J: Large ribosomal subunit protein uL13
S: Large ribosomal subunit protein uL22
U: Large ribosomal subunit protein uL24
Y: Large ribosomal subunit protein uL29


Theoretical massNumber of molelcules
Total (without water)1,103,92412
Polymers1,103,92412
Non-polymers00
Water00
1


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

-
Components

-
Large ribosomal subunit protein ... , 10 types, 10 molecules QRT2DEJSUY

#1: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7L3
#2: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG48
#3: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10144.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ0
#4: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 4290.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7P5
#7: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P60438
#8: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P60723
#9: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AA10
#10: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P61175
#11: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11078.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P60624
#12: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7087.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7M6

-
Protein / RNA chain , 2 types, 2 molecules ACA

#5: Protein Ribosomal large subunit pseudouridine synthase B / 23S rRNA pseudouridine(2605) synthase / rRNA pseudouridylate synthase B / rRNA-uridine isomerase B


Mass: 32010.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria)
References: UniProt: P37765, 23S rRNA pseudouridine2605 synthase
#6: RNA chain 23S rRNA


Mass: 941625.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Base U at position 2605 on 23S rRNA (Chain CA:1281) could also be PSU.
Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 802133627

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: WT 12C 50S ribosomal subunit assembly intermediate / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW25113
Buffer solutionpH: 7.5
Details: Most of the sucrose was removed by spin concentration.
Buffer component
IDConc.NameFormulaBuffer-ID
150.0 mMTris HydrochlorideC4H11NO31
2100.0 mMAmmonium ChlorideNH4Cl1
310.0 mMMagnesium ChlorideMgCl21
40.5 mMEthylenediaminetetraacetic AcidC10H16N2O81
56.0 mMBeta-mercaptoethanolC2H6OS1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K / Details: 3 microliter of the sample was added.

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Details: In order to account for highly preferred orientation of the specimen, data were acquired using tilts at -20 degrees.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 5 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
7UCSF ChimeraXmodel fitting
12cryoSPARC3D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionDetails: CTF correction were performed by Patch CTF Estimation of cryoSPARC
Type: NONE
3D reconstructionResolution: 5.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22502 / Symmetry type: POINT
Atomic model buildingB value: 118.8 / Protocol: OTHER / Space: REAL / Target criteria: Comprehensive validation (cryo-EM)
Details: The atomic model was fitted into a low resolution (5 angstrom) EM map; therefore the coordinates should only serve as a general visual representation and should not be looked into detail. ...Details: The atomic model was fitted into a low resolution (5 angstrom) EM map; therefore the coordinates should only serve as a general visual representation and should not be looked into detail. Initial docking of the atomic model was done in ChimeraX. Coot and Phenix were used for real-space refinements. Geometry minimization in Phenix was used to improve the RNA atomic model.
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-IDSource nameType
14YBB

4ybb

CA4YBBCA1PDBexperimental model
28RPY

8rpy

28RPY22PDBexperimental model
38RPY

8rpy

D8RPYD2PDBexperimental model
48RPY

8rpy

E8RPYE2PDBexperimental model
58RPY

8rpy

J8RPYJ2PDBexperimental model
68RPY

8rpy

Q8RPYQ2PDBexperimental model
78RPY

8rpy

R8RPYR2PDBexperimental model
88RPY

8rpy

S8RPYS2PDBexperimental model
98RPY

8rpy

T8RPYT2PDBexperimental model
108RPY

8rpy

U8RPYU2PDBexperimental model
118RPY

8rpy

Y8RPYY2PDBexperimental model
12AF-A0A828LEY7-F1A3AlphaFoldin silico model

+
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