[English] 日本語
Yorodumi
- PDB-7wto: Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Ts... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wto
TitleCryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-1 (without Rps2)
Components
  • (40S ribosomal protein ...) x 14
  • 18S rRNA
  • Pre-rRNA-processing protein PNO1
KeywordsRIBOSOME / ribosome biogenesis / 40S ribosome
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Negative regulators of DDX58/IFIH1 signaling / mTORC1-mediated signalling / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit ...endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Negative regulators of DDX58/IFIH1 signaling / mTORC1-mediated signalling / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / regulation of translational fidelity / Ub-specific processing proteases / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / unfolded protein binding / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Krr1, KH1 domain / Krr1 KH1 domain / K Homology domain, type 1 superfamily / : / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S7e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. ...Krr1, KH1 domain / Krr1 KH1 domain / K Homology domain, type 1 superfamily / : / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S7e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / : / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S4/S9 N-terminal domain / 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 S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / Ribosomal protein S11 / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein L23/L15e core domain superfamily / Zinc-binding ribosomal protein / KOW motif / KOW / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCheng, J. / Lau, B. / Thoms, M. / Ameismeier, M. / Berninghausen, O. / Hurt, E. / Beckmann, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2022
Title: The nucleoplasmic phase of pre-40S formation prior to nuclear export.
Authors: Jingdong Cheng / Benjamin Lau / Matthias Thoms / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann /
Abstract: Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural ...Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.
History
DepositionFeb 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C2: 18S rRNA
SB: 40S ribosomal protein S1-A
SE: 40S ribosomal protein S4-A
SG: 40S ribosomal protein S6-A
SH: 40S ribosomal protein S7-A
SI: 40S ribosomal protein S8-A
SJ: 40S ribosomal protein S9-A
SL: 40S ribosomal protein S11-A
SN: 40S ribosomal protein S13
SO: 40S ribosomal protein S14-A
SW: 40S ribosomal protein S22-A
SX: 40S ribosomal protein S23-A
SY: 40S ribosomal protein S24-A
Sb: 40S ribosomal protein S27-A
Se: 40S ribosomal protein S30-A
CA: Pre-rRNA-processing protein PNO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)873,74017
Polymers873,67516
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
40S ribosomal protein ... , 14 types, 14 molecules SBSESGSHSISJSLSNSOSWSXSYSbSe

#2: Protein 40S ribosomal protein S1-A / RP10A / Small ribosomal subunit protein eS1-A


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33442
#3: Protein 40S ribosomal protein S4-A / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#4: Protein 40S ribosomal protein S6-A / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX37
#5: Protein 40S ribosomal protein S7-A / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P26786
#6: Protein 40S ribosomal protein S8-A / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#7: Protein 40S ribosomal protein S9-A / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O13516
#8: Protein 40S ribosomal protein S11-A / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#9: Protein 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05756
#10: Protein 40S ribosomal protein S14-A / RP59A / Small ribosomal subunit protein uS11-A


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P06367
#11: Protein 40S ribosomal protein S22-A / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1
#12: Protein 40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#13: Protein 40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#14: Protein 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P35997
#15: Protein 40S ribosomal protein S30-A / Small ribosomal subunit protein eS30-A


Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX33

-
RNA chain / Protein / Non-polymers , 3 types, 3 molecules C2CA

#16: Protein Pre-rRNA-processing protein PNO1 / Partner of NOB1 / Ribosomal RNA-processing protein 20


Mass: 30380.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q99216
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#1: RNA chain 18S rRNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Yeast pre-40S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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 / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CTF correctionDetails: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59786 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 84.82 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004847844
ELECTRON MICROSCOPYf_angle_d0.825870386
ELECTRON MICROSCOPYf_chiral_restr0.04418882
ELECTRON MICROSCOPYf_plane_restr0.00694494
ELECTRON MICROSCOPYf_dihedral_angle_d15.525717015

+
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