[English] 日本語
Yorodumi
- PDB-6gc6: 50S ribosomal subunit assembly intermediate state 2 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6gc6
Title50S ribosomal subunit assembly intermediate state 2
Components
  • (50S ribosomal protein ...) x 18
  • 23S ribosomal RNA
KeywordsRIBOSOME / assembly precursor 48S 50S biogenesis in vitro reconstitution
Function / homologyRibosomal protein L34, conserved site / Ribosomal protein L3, conserved site / Ribosomal protein L15 / Ribosomal protein L21-like / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L18e/L15P ...Ribosomal protein L34, conserved site / Ribosomal protein L3, conserved site / Ribosomal protein L15 / Ribosomal protein L21-like / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L18e/L15P / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L29/L35 superfamily / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L2, domain 3 / Ribosomal protein L2, domain 2 / Ribosomal protein L25/L23 / 50S ribosomal protein uL4 / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L20, C-terminal / L21-like superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein L30p/L7e / Ribosomal protein L19 / Ribosomal protein L17 / Ribosomal L29 protein / Ribosomal prokaryotic L21 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L4/L1 family / Ribosomal protein L13 / Ribosomal protein L34 / KOW motif / Ribosomal protein L20 / Ribosomal protein L6 / Ribosomal protein L3 / Ribosomal L18e/L15P superfamily / Ribosomal protein L23 / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L19 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Zinc-binding ribosomal protein / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L15 signature. / Ribosomal protein L17 / Translation protein, beta-barrel domain superfamily / Ribosomal protein L14P / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L6 signature 1. / Ribosomal protein L6 / Ribosomal protein L29 signature. / Ribosomal protein L30 signature. / Ribosomal protein L13 signature. / Ribosomal protein L34 signature. / Ribosomal protein L20 signature. / Ribosomal protein L19 signature. / Ribosomal protein L24 signature. / Ribosomal protein L17 signature. / Ribosomal protein L21 signature. / Ribosomal protein L3 / Ribosomal protein L34 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L22/L17 / Translation protein SH3-like domain superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L24/L26, conserved site / KOW / Ribosomal protein L13, bacterial-type / Ribosomal protein L13 / Ribosomal protein L20 / Ribosomal protein L15, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L6, conserved site / Ribosomal protein L19 / Ribosomal protein L15, conserved site / Ribosomal protein L21 / Ribosomal protein L29/L35
Function and homology information
Specimen sourceEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsNikolay, R. / Hilal, T. / Qin, B. / Loerke, J. / Buerger, J. / Mielke, T. / Spahn, C.M.T.
CitationJournal: Mol. Cell / Year: 2018
Title: Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution.
Authors: Rainer Nikolay / Tarek Hilal / Bo Qin / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kathrin Textoris-Taube / Knud H Nierhaus / Christian M T Spahn
Abstract: The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ...The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ribosome assembly, our mechanistic comprehension of this process is still limited. Here, we perform an in vitro reconstitution of the Escherichia coli 50S ribosomal subunit. Late reconstitution products were subjected to high-resolution cryo-electron microscopy and multiparticle refinement analysis to reconstruct five distinct precursors of the 50S subunit with 4.3-3.8 Å resolution. These assembly intermediates define a progressive maturation pathway culminating in a late assembly particle, whose structure is more than 96% identical to a mature 50S subunit. Our structures monitor the formation and stabilization of structural elements in a nascent particle in unprecedented detail and identify the maturation of the rRNA-based peptidyl transferase center as the final critical step along the 50S assembly pathway.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 17, 2018 / Release: Jul 4, 2018

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4381
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 23S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
G: 50S ribosomal protein L6
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
N: 50S ribosomal protein L17
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
Y: 50S ribosomal protein L29
0: 50S ribosomal protein L32
2: 50S ribosomal protein L34
Z: 50S ribosomal protein L30


Theoretical massNumber of molelcules
Total (without water)1,184,45819
Polyers1,184,45819
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 1 types, 1 molecules A

#1: RNA chain 23S ribosomal RNA /


Mass: 941612.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 1063812051

+
50S ribosomal protein ... , 18 types, 18 molecules CDEGJKLNPQRSTUY02Z

#2: Protein/peptide 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 24213.004 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P60422
#3: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


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


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P60723
#5: Protein/peptide 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG55
#6: Protein/peptide 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AA10
#7: Protein/peptide 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0ADY3
#8: Protein/peptide 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P02413
#9: Protein/peptide 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG44
#10: Protein/peptide 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7K6
#11: Protein/peptide 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


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


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG48
#13: Protein/peptide 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P61175
#14: Protein/peptide 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ0
#15: Protein/peptide 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


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


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7M6
#17: Protein/peptide 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7N4
#18: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7P5
#19: Protein/peptide 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG51

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 50S ribosomal subunit in vitro assembly intermediate state 2
Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19
Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.11_2561: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
7UCSF Chimeramodel fitting
9SPIDER14initial Euler assignment
10SPIDER14final Euler assignment
11SPIDER14classification
12SPIDER143D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 235068
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 16754 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00267012
ELECTRON MICROSCOPYf_angle_d0.629100893
ELECTRON MICROSCOPYf_dihedral_angle_d14.87135406
ELECTRON MICROSCOPYf_chiral_restr0.03113005
ELECTRON MICROSCOPYf_plane_restr0.0054966

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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