[English] 日本語
Yorodumi
- EMDB-6697: Cryo-EM structure of the 90S small subunit pre-ribosome (Noc4-TAP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6697
TitleCryo-EM structure of the 90S small subunit pre-ribosome (Noc4-TAP)
Map data
Sample
  • Complex: 90S small subunit pre-ribosome (Noc4-TAP)
Function / homology
Function and homology information


regulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear microtubule / Pwp2p-containing subcomplex of 90S preribosome ...regulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear microtubule / Pwp2p-containing subcomplex of 90S preribosome / box C/D sno(s)RNA binding / Mpp10 complex / rRNA modification / rRNA (pseudouridine) methyltransferase activity / snoRNA guided rRNA 2'-O-methylation / septum digestion after cytokinesis / histone H2AQ104 methyltransferase activity / rRNA 2'-O-methylation / snRNA binding / box C/D sno(s)RNA 3'-end processing / regulation of rRNA processing / rRNA methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA folding chaperone / rDNA heterochromatin / U4/U6 snRNP / box C/D methylation guide snoRNP complex / tRNA export from nucleus / single-stranded telomeric DNA binding / : / translational readthrough / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / O-methyltransferase activity / rRNA base methylation / SUMOylation of RNA binding proteins / protein localization to nucleolus / rRNA methylation / mTORC1-mediated signalling / U4 snRNA binding / Protein hydroxylation / U4 snRNP / 90S preribosome assembly / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / poly(U) RNA binding / Translation initiation complex formation / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Ribosomal scanning and start codon recognition / poly(A)+ mRNA export from nucleus / precatalytic spliceosome / snoRNA binding / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / establishment of cell polarity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of transcription by RNA polymerase I / 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) / spliceosomal complex assembly / L13a-mediated translational silencing of Ceruloplasmin expression / nucleolar large rRNA transcription by RNA polymerase I / Ub-specific processing proteases / 90S preribosome / ribosomal subunit export from nucleus / U4/U6 x U5 tri-snRNP complex / proteasome assembly / regulation of translational fidelity / 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) / RNA endonuclease activity / ribosomal small subunit export from nucleus / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome assembly / spliceosomal complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / mRNA splicing, via spliceosome / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / enzyme activator activity / cytoplasmic stress granule / protein tag activity / rRNA processing / : / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation
Similarity search - Function
rRNA biogenesis protein Rrp5 / : / : / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / : / WD repeat-containing protein 75 second beta-propeller ...rRNA biogenesis protein Rrp5 / : / : / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / : / WD repeat-containing protein 75 second beta-propeller / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Nrap protein domain 1 / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / rRNA-processing protein Fcf1, PIN domain / rRNA-processing protein Fcf1/Utp23 / Fcf1 / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / BP28, C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / : / BP28CT (NUC211) domain / NOP5NT (NUC127) domain / U3 small nucleolar RNA-associated protein 10 / HEATR1-like, HEAT repeats / BP28CT (NUC211) domain / : / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Small-subunit processome, Utp21 / : / Utp21 specific WD40 associated putative domain / WDR36/Utp21 second beta-propeller domain / WDR36/Utp21 first beta-propeller / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Mpp10 protein / Ribosomal RNA-processing protein Rrp9-like / RNA 3'-terminal phosphate cyclase type 2 / RNA 3'-terminal phosphate cyclase / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Nucleolar protein Nop56/Nop58 / RNA 3'-terminal phosphate cyclase / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Krr1, KH1 domain / Krr1 KH1 domain / PRP39 N-terminal HAT repeat / Bystin / Bystin / Anaphase-promoting complex subunit 4, WD40 domain / Large family of predicted nucleotide-binding domains / U3 snoRNP protein/Ribosome production factor 1 / : / : / Anaphase-promoting complex subunit 4 WD40 domain / Eukaryotic type KH-domain (KH-domain type I) / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / PIN domain / NOSIC
Similarity search - Domain/homology
Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / 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 uS4A / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / 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 uS9A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / Periodic tryptophan protein 2 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / U3 small nucleolar ribonucleoprotein protein IMP3 / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / Small ribosomal subunit protein eS12 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar ribonucleoprotein protein IMP4 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / rRNA processing protein RCL1 / Ribosome biogenesis protein BMS1 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / Small ribosomal subunit protein eS28A / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsYe K / Zhu X / Sun Q
CitationJournal: Elife / Year: 2017
Title: Molecular architecture of the 90S small subunit pre-ribosome.
Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye /
Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
History
DepositionJan 16, 2017-
Header (metadata) releaseMar 29, 2017-
Map releaseMar 29, 2017-
UpdateMar 29, 2017-
Current statusMar 29, 2017Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6697.png

Downloads & links

-
Map

FileDownload / File: emd_6697.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 480 pix.
= 681.6 Å		1.42 Å/pix.
x 480 pix.
= 681.6 Å		1.42 Å/pix.
x 480 pix.
= 681.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.05033438 - 0.12918253
Average (Standard dev.)0.00035046774 (±0.0073576695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 681.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z681.600681.600681.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0500.1290.000

-
Supplemental data

-
Sample components

-
Entire : 90S small subunit pre-ribosome (Noc4-TAP)

EntireName: 90S small subunit pre-ribosome (Noc4-TAP)
Components
  • Complex: 90S small subunit pre-ribosome (Noc4-TAP)

-
Supramolecule #1: 90S small subunit pre-ribosome (Noc4-TAP)

SupramoleculeName: 90S small subunit pre-ribosome (Noc4-TAP) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMCH3COOKpotassium acetate
20.0 mMHEPES-KHEPES-K
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsOD280=2.0

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 1769 / Average exposure time: 1.6 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 98592 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 127198
CTF correctionSoftware - Name: CTFFIND3
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Relion (ver. 1.3) / Number images used: 12643
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: Relion (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Relion (ver. 1.3) / Details: use the default parameters of Relion
Final 3D classificationNumber classes: 2 / Avg.num./class: 20000
FSC plot (resolution estimation)

+
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