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- EMDB-10836: Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10836
TitleRix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)
Map dataRix1-subcomplex of the Rix1-Rea1 pre-60S particle
Sample
  • Complex: Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex
    • Protein or peptide: Pre-rRNA-processing protein IPI3
    • Protein or peptide: Pre-rRNA-processing protein RIX1
    • Protein or peptide: Pre-rRNA-processing protein IPI1
Keywordspre-60S / Biogenesis / LSU / Large subunit / ribosome assembly / RIBOSOME
Function / homology
Function and homology information


rixosome complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear pre-replicative complex / regulation of DNA-templated DNA replication initiation / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-templated DNA replication / rRNA processing / ribosomal large subunit assembly / chromatin binding ...rixosome complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear pre-replicative complex / regulation of DNA-templated DNA replication initiation / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-templated DNA replication / rRNA processing / ribosomal large subunit assembly / chromatin binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Pre-rRNA-processing protein Ipi1, N-terminal / Rix1 complex component involved in 60S ribosome maturation / Pre-rRNA-processing protein RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...Pre-rRNA-processing protein Ipi1, N-terminal / Rix1 complex component involved in 60S ribosome maturation / Pre-rRNA-processing protein RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Pre-rRNA-processing protein IPI1 / Pre-rRNA-processing protein IPI1 / Pre-rRNA-processing protein RIX1 / Pre-rRNA-processing protein IPI3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKater L / Beckmann R
CitationJournal: Mol Cell / Year: 2020
Title: Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Authors: Lukas Kater / Valentin Mitterer / Matthias Thoms / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering ...Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1-Ipi3 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
History
DepositionApr 7, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yle
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yle
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10836.png

Downloads & links

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Map

FileDownload / File: emd_10836.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRix1-subcomplex of the Rix1-Rea1 pre-60S particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 211.8 Å		1.06 Å/pix.
x 200 pix.
= 211.8 Å		1.06 Å/pix.
x 200 pix.
= 211.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.037551817 - 0.072617956
Average (Standard dev.)0.00043897267 (±0.0037487403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z211.800211.800211.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0380.0730.000

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Supplemental data

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Half map: Relion half map (unfiltered, unmasked)

Fileemd_10836_half_map_1.map
AnnotationRelion half map (unfiltered, unmasked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion half map (unfiltered, unmasked)

Fileemd_10836_half_map_2.map
AnnotationRelion half map (unfiltered, unmasked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex

EntireName: Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex
Components
  • Complex: Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex
    • Protein or peptide: Pre-rRNA-processing protein IPI3
    • Protein or peptide: Pre-rRNA-processing protein RIX1
    • Protein or peptide: Pre-rRNA-processing protein IPI1

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Supramolecule #1: Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex

SupramoleculeName: Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Rix1-TAP Flag-Rea1 derived pre-60S assembly complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Pre-rRNA-processing protein IPI3

MacromoleculeName: Pre-rRNA-processing protein IPI3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 61.836695 KDa
SequenceString: MDEQVIFTTN TSGTIASVHS FEQINLRQCS TQSRNSCVQV GNKYLFIAQA QKALINVYNL SGSFKRESVE QRLPLPEILK CLEVVENDG VQYDRIQGVN HNLPDFNLPY LLLGSTESGK LYIWELNSGI LLNVKPMAHY QSITKIKSIL NGKYIITSGN D SRVIIWQT ...String:
MDEQVIFTTN TSGTIASVHS FEQINLRQCS TQSRNSCVQV GNKYLFIAQA QKALINVYNL SGSFKRESVE QRLPLPEILK CLEVVENDG VQYDRIQGVN HNLPDFNLPY LLLGSTESGK LYIWELNSGI LLNVKPMAHY QSITKIKSIL NGKYIITSGN D SRVIIWQT VDLVSASNDD PKPLCILHDH TLPVTDFQVS SSQGKFLSCT DTKLFTVSQD ATIRCYDLSL IGSKKKQKAN EN DVSIGKT PVLLATFTTP YSIKSIVLDP ADRACYIGTA EGCFSLNLFY KLKGNAIVNL LQSAGVNTVQ KGRVFSLVQR NSL TGGENE DLDALYAMGQ LVCENVLNSN VSCLEISMDG TLLLIGDTEG KVSIAEIYSK QIIRTIQTLT TSQDSVGEVT NLLT NPYRL ERGNLLFEGE SKGKQPSNNN GHNFMKIPNL QRVIFDGKNK GHLHDIWYQI GEPEAETDPN LALPLNDFNA YLEQV KTQE SIFSHIGKVS SNVKVIDNKI DATSSLDSNA AKDEEITELK TNIEALTHAY KELRDMHEKL YEEHQQMLDK Q

UniProtKB: Pre-rRNA-processing protein IPI3

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Macromolecule #2: Pre-rRNA-processing protein RIX1

MacromoleculeName: Pre-rRNA-processing protein RIX1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 86.839844 KDa
SequenceString: MSEEFIAVST LARNLEIAKG NEFHTILATL RSPVYINEQL LKSELSFLVT KILKLIRSGN DFDLWKGCHT SVVTCAYNPL VLSTHGGQL LAAIYSRLEQ KTGFYSSVIS SSHGKQLFNT LISSVAIIID LMKNKPTLSR EALVPKLKAI IPTLITLSQY E PELVLPVL ...String:
MSEEFIAVST LARNLEIAKG NEFHTILATL RSPVYINEQL LKSELSFLVT KILKLIRSGN DFDLWKGCHT SVVTCAYNPL VLSTHGGQL LAAIYSRLEQ KTGFYSSVIS SSHGKQLFNT LISSVAIIID LMKNKPTLSR EALVPKLKAI IPTLITLSQY E PELVLPVL QRILKRNTTT FKPFTNKFRT VLINLIISDY ASLGTKTQRL VCENFAYLHL LKIQVSDTSD DETQAHHKIY AD SNWRTGL MSILSQFKPI IQLCGEILDF EQDNELYKLI KSLPVIDESN NKEEFLPSLK LDFNAPLTLW EIPQRLSLLA DML VAFISL PTPFPIRVPL GGINSLCEVL LGVSNKYLPL KKELRHDNEL NGVINTILPQ IQFQGIRLWE IMVSKYGKCG LSFF EGILS SIELFIPLKK KSNNEIDFNV VGSLKFEFAT VFRLVNMILS HLGHQLNIIS VISQLIEVAL FLSHDKTLID SLFKN RKSI MKQQTKTKQS KRSKSAEGAF SDIYTHPELF VCKNSMNWFN EINDFFITAL NNWILPSTPH IQILKYSITQ SLRLKE RFG YIPESFVNLL RCEVLHPGSE RVSILPIAIS LLKNINDDMF ELLCHPKVPV GMVYQLHKPL DLGEDGEVRD DINKKEV ET NESSSNANTG LETLKALENL ENVTIPEPKH EVPKVVDDTA IFKKRSVEEV IERESTSSHK KVKFVEETTV DNGEELIV K KAVSQTKEEE KPMEDSEDEE QEEFEIPAIE LSDDEEEEEE EE

UniProtKB: Pre-rRNA-processing protein RIX1

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Macromolecule #3: Pre-rRNA-processing protein IPI1

MacromoleculeName: Pre-rRNA-processing protein IPI1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.928895 KDa
SequenceString: MTKSRKQKQK KQDFLRKKLK VGKPKEKARN ATDTSFVSKT ISIRNQHLDQ NPHDLTKRLT LLKHHNINVR KETLTTFQKS IPSIIKSRL MTPLLTQSIP LICDESQQVR QGLIDLVDEI GSHDAEILKL HCNIFVLYIN MAMTHIVTQI QADSTKFLSH L LKYCGDEV ...String:
MTKSRKQKQK KQDFLRKKLK VGKPKEKARN ATDTSFVSKT ISIRNQHLDQ NPHDLTKRLT LLKHHNINVR KETLTTFQKS IPSIIKSRL MTPLLTQSIP LICDESQQVR QGLIDLVDEI GSHDAEILKL HCNIFVLYIN MAMTHIVTQI QADSTKFLSH L LKYCGDEV VRKSWVKLLN GVFGVLGWGQ VGKNDSASIV QTKKRNAKYV TIHLNALYTL VEYGCQDERA RSDGDTAETT ED SGTLRNP YLIPDYPQPF EHLKLFTREL KVQDATSSGV NATLLSLATQ DIDTRKAVFI EQFLPIVRKK IEVIIKEGGE CGK SANKLK TLLAKIFD

UniProtKB: Pre-rRNA-processing protein IPI1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 273799
Startup modelType of model: EMDB MAP
EMDB ID:

3199

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 114398
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6yle:
Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)

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