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- PDB-6gc0: 50S ribosomal subunit assembly intermediate state 4 -

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Basic information

Entry
Database: PDB / ID: 6gc0
Title50S ribosomal subunit assembly intermediate state 4
Components
  • (50S ribosomal protein ...) x 26
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / assembly precursor 48S 50S biogenesis in vitro reconstitution
Function / homologyRibosomal protein L2, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, N-terminal ...Ribosomal protein L2, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, N-terminal / Ribosomal protein L2, C-terminal / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L3 signature. / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L14 superfamily / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L27, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein L25, short-form / Ribosomal protein L35 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L9, N-terminal domain / Ribosomal prokaryotic L21 protein / Ribosomal L28 family / Ribosomal L29 protein / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / Ribosomal protein L17 / Ribosomal protein L19 / Ribosomal L25p family / ribosomal L5P family C-terminus / Ribosomal protein L35 / Ribosomal L32p protein family / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L9, C-terminal domain / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L5 signature. / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L4/L1 family / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L23 / Ribosomal protein L13 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L6 / Ribosomal protein L20 / KOW motif / Ribosomal protein L34 / Ribosomal protein L33 / Ribosomal protein L22/L17, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L14P / Ribosomal protein L21 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L33 / Ribosomal protein L27 / Ribosomal protein L28 / Ribosomal protein L29, conserved site / Ribosomal protein L22/L17 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L6 / Ribosomal protein L3 / Ribosomal protein L17 / Ribosomal protein L34 / Ribosomal protein L9 / Ribosomal protein L15 signature.
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsNikolay, R. / Hilal, T. / Qin, B. / Loerke, J. / Buerger, J. / Mielke, T. / Spahn, C.M.T.
Funding supportGermany , 2 items
OrganizationGrant numberCountry
German Research FoundationFOR1805Germany
German Research FoundationSFB740Germany
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 16, 2018 / Release: Jun 20, 2018

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Structure visualization

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  • EMDB-4379
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Assembly

Deposited unit
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
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
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35


Theoretical massNumber of molelcules
Total (without water)1,307,47828
Polyers1,307,47828
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, equilibrium centrifugation
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TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S ribosomal RNA /


Mass: 941612.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 991970073
#2: RNA chain 5S ribosomal RNA /


Mass: 38483.926 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1352767907

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50S ribosomal protein ... , 26 types, 26 molecules CDEFGHJKLNOPQRSTUVWXYZ0123

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


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#4: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


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


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#6: Protein/peptide 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#7: Protein/peptide 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#8: Protein/peptide 50S ribosomal protein L9 / / Large ribosomal subunit protein bL9


Mass: 5467.367 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#9: Protein/peptide 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


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


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


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


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#13: Protein/peptide 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#14: Protein/peptide 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


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


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


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


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


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


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#20: Protein/peptide 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#21: Protein/peptide 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 8275.498 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#22: Protein/peptide 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#23: Protein/peptide 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#24: Protein/peptide 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#25: Protein/peptide 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#26: Protein/peptide 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 5814.842 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#27: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#28: Protein/peptide 50S ribosomal protein L35 / / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 50S ribosomal subunit assembly intermediate state 4 / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28
Source: NATURAL
Molecular weightValue: 1.5 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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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 / Nominal magnification: 31000 / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 5 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 1684
Image scansMovie frames/image: 25 / Used frames/image: 1-25

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Processing

SoftwareName: PHENIX / Version: dev_2415: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4SPIDER14CTF correction
7UCSF Chimera1.11model fitting
8Coot0.8.4model fitting
10SPIDER14initial Euler assignment
11SPIDER14final Euler assignment
12SPIDER14classification
13SPIDER143D reconstruction
14PHENIX1.11model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 154462
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 37815 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00291786
ELECTRON MICROSCOPYf_angle_d0.484138070
ELECTRON MICROSCOPYf_dihedral_angle_d13.96354335
ELECTRON MICROSCOPYf_chiral_restr0.02817737
ELECTRON MICROSCOPYf_plane_restr0.0056884

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