6GC0

50S ribosomal subunit assembly intermediate state 4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution.

Nikolay, R.Hilal, T.Qin, B.Mielke, T.Burger, J.Loerke, J.Textoris-Taube, K.Nierhaus, K.H.Spahn, C.M.T.

(2018) Mol Cell 70: 881-893.e3

  • DOI: 10.1016/j.molcel.2018.05.003
  • Structures With Same Primary Citation

  • PubMed 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 ribosome assembly, our mechanistic comprehension of th ...

    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.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany. Electronic address: christian.spahn@charite.de.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
143Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
116Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coliMutation(s): 0 
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
93Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
102Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
76Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Escherichia coliMutation(s): 0 
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
58Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
56Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
50Escherichia coliMutation(s): 0 
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
271Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
177Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
50Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10

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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAA2904Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAB119Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanySFB740

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Other