[English] 日本語
Yorodumi
- EMDB-24412: Ytm1 associated nascent 60S class 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24412
TitleYtm1 associated nascent 60S class 3
Map dataYtm1 associated nascent 60S class 3
Sample
  • Complex: nascent 60S
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / cytosolic large ribosomal subunit assembly / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome / PeBoW complex ...Major pathway of rRNA processing in the nucleolus and cytosol / cytosolic large ribosomal subunit assembly / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome / PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / preribosome, large subunit precursor / protein-RNA complex assembly / ribonucleoprotein complex binding / maturation of LSU-rRNA / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / nucleolus / chromatin / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
WD repeat WDR12/Ytm1 / Mak16 protein / Mak16 protein C-terminal region / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / NLE / NLE (NUC135) domain / Pescadillo ...WD repeat WDR12/Ytm1 / Mak16 protein / Mak16 protein C-terminal region / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / NLE / NLE (NUC135) domain / Pescadillo / Pescadillo N-terminus / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / breast cancer carboxy-terminal domain / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / : / : / Ribosomal protein L6e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / BRCT domain profile. / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / BRCT domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L30e, conserved site / Ribosomal Protein L6, KOW domain / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / : / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L7A/L8 / BRCT domain superfamily / 60S ribosomal protein L6E / 60S ribosomal protein L35 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal protein L31e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L31e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain
Similarity search - Domain/homology
Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein uL13B / Pescadillo homolog / Large ribosomal subunit protein eL13 / Ribosome biogenesis protein erb1 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein uL29 ...Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein uL13B / Pescadillo homolog / Large ribosomal subunit protein eL13 / Ribosome biogenesis protein erb1 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL36B / Large ribosomal subunit protein eL37B / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL2A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein uL30B / Large ribosomal subunit protein uL15A / Large ribosomal subunit protein uL3A / Large ribosomal subunit protein uL18A / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL32A / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL16A / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL23A / Ribosome biogenesis protein rlp24 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein uL4B / Large ribosomal subunit protein eL31 / Ribosome biogenesis protein ytm1 / Large ribosomal subunit protein eL33B / Large ribosomal subunit protein eL38A / Protein mak16 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL30B / Large ribosomal subunit protein eL21A
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBilokapic S / Halic M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141694 United States
CitationJournal: Mol Cell / Year: 2022
Title: Chromatin localization of nucleophosmin organizes ribosome biogenesis.
Authors: Ilaria Ugolini / Silvija Bilokapic / Mylene Ferrolino / Josiah Teague / Yinxia Yan / Xuelin Zhou / Ashish Deshmukh / Michael White / Richard W Kriwacki / Mario Halic /
Abstract: Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin ...Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.
History
DepositionJul 9, 2021-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_24412.png

Downloads & links

-
Map

FileDownload / File: emd_24412.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYtm1 associated nascent 60S class 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.49211872 - 0.87022364
Average (Standard dev.)0.00047574658 (±0.0149194505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : nascent 60S

EntireName: nascent 60S
Components
  • Complex: nascent 60S

-
Supramolecule #1: nascent 60S

SupramoleculeName: nascent 60S / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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