9HC4 | pdb_00009hc4

Cryo-EM structure of P. urativorans 70S ribosome with 2 copies of bS20.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Structurally heterogeneous ribosomes cooperate in protein synthesis in bacterial cells.

Helena-Bueno, K.Kopetschke, S.Filbeck, S.Chan, L.I.Birsan, S.Basle, A.Hudson, M.Pfeffer, S.Hill, C.H.Melnikov, S.V.

(2025) Nat Commun 16: 2751-2751

  • DOI: https://doi.org/10.1038/s41467-025-57955-8
  • Primary Citation of Related Structures:  
    9HC4

  • PubMed Abstract: 

    Ribosome heterogeneity is a paradigm in biology, pertaining to the existence of structurally distinct populations of ribosomes within a single organism or cell. This concept suggests that structurally distinct pools of ribosomes have different functional properties and may be used to translate specific mRNAs. However, it is unknown to what extent structural heterogeneity reflects genuine functional specialization rather than stochastic variations in ribosome assembly. Here, we address this question by combining cryo-electron microscopy and tomography to observe individual structurally heterogeneous ribosomes in bacterial cells. We show that 70% of ribosomes in Psychrobacter urativorans contain a second copy of the ribosomal protein bS20 at a previously unknown binding site on the large ribosomal subunit. We then determine that this second bS20 copy appears to be functionally neutral. This demonstrates that ribosome heterogeneity does not necessarily lead to functional specialization, even when it involves significant variations such as the presence or absence of a ribosomal protein. Instead, we show that heterogeneous ribosomes can cooperate in general protein synthesis rather than specialize in translating discrete populations of mRNA.


  • Organizational Affiliation

    Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9A [auth F]128Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9B [auth C1]166Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18C [auth R3]76Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2D [auth A4]269Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5E [auth E5]171Psychrobacter urativoransMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12F [auth L6]124Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5G [auth F7]178Psychrobacter urativoransMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4H [auth E9]200Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for A0A0M4U627 (Psychrobacter urativorans)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32I [auth aA]60Psychrobacter urativoransMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17J [auth MB]119Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25K [auth UC]219Psychrobacter urativoransMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28L [auth WD]78Psychrobacter urativoransMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29M [auth XE]65Psychrobacter urativoransMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22N [auth RF]109Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6O [auth FG]134Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27P [auth VH]85Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24Q [auth TI]105Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31BR [auth fJ]93Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14S [auth HK]101Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15T [auth OL]88Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13U [auth MM]118Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20V [auth PO]118Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19W [auth SP]91Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for Q4FUF2 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8X [auth BQ]132Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6Y [auth GR]177Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7Z [auth GS]157Psychrobacter urativoransMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3AA [auth CT]241Psychrobacter urativoransMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11BA [auth KU]129Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21CA [auth NV]71Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30DA [auth YW]59Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13EA [auth IX]142Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10FA [auth JY]103Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17GA [auth QZ]91Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34HA [auth Ba]44Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21IA [auth Qb]103Psychrobacter urativoransMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18JA [auth Nc]116Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15KA [auth Kd]146Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14LA [auth Je]122Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3MA [auth Af]212Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16NA [auth Lg]137Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35OA [auth dh]65Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for Q4FQ63 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19PA [auth Oi]130Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for Q4FQ45 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16QA [auth Pj]89Psychrobacter urativoransMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33RA [auth bk]51Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for A0A0M4SWV1 (Psychrobacter urativorans)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2SA [auth Cl]274Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for Q4FUF3 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4TA [auth Dm]213Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for Q4FUD2 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23UA [auth Sn]116Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for Q4FUF4 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20VA [auth To],
XA [auth A]
88Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for Q4FRM3 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36WA [auth ep]38Psychrobacter urativoransMutation(s): 0 
UniProt
Find proteins for Q4FUD5 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
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Entity ID: 50
MoleculeChains LengthOrganismImage
5S rRNAYA [auth D8]115Psychrobacter urativorans
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Entity ID: 51
MoleculeChains LengthOrganismImage
16S rRNAZA [auth iN]1,589Psychrobacter urativorans
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Entity ID: 52
MoleculeChains LengthOrganismImage
23S rRNAAB [auth Z2]2,882Psychrobacter urativorans
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal SocietyUnited KingdomRGS/R2/202003

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references