5ZET

M. smegmatis P/P state 50S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA.

Mishra, S.Ahmed, T.Tyagi, A.Shi, J.Bhushan, S.

(2018) Sci Rep 8: 13587-13587

  • DOI: 10.1038/s41598-018-31850-3
  • Primary Citation of Related Structures:  
    5ZEY, 5ZEP, 5ZEU, 5ZET, 5ZEB

  • PubMed Abstract: 
  • Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action ...

    Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 Å, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.


    Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore. sbhushan@ntu.edu.sg.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2A [auth C]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplBMSMEG_1439MSMEI_1403
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Entity ID: 2
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50S ribosomal protein L3B [auth D]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplCMSMEG_1436MSMEI_1400
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth E]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplDMSMEG_1437MSMEI_1401
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5D [auth F]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplEMSMEG_1467MSMEI_1431
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6E [auth G]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplFMSMEG_1470MSMEI_1434
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Entity ID: 6
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50S ribosomal protein L9F [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplIMSMEG_6894MSMEI_6710
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Entity ID: 7
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50S ribosomal protein L10G [auth I]175Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplJMSMEG_1364MSMEI_1325
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Entity ID: 8
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50S ribosomal protein L11H [auth J]142Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplKMSMEG_1346MSMEI_1308
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Entity ID: 9
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50S ribosomal protein L13I [auth K]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplMMSMEG_1556MSMEI_1519
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Entity ID: 10
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50S ribosomal protein L14J [auth L]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplNMSMEG_1465MSMEI_1429
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Entity ID: 11
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50S ribosomal protein L15K [auth M]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplOMSMEG_1474
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Entity ID: 12
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50S ribosomal protein L16L [auth N]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplPMSMEG_1443MSMEI_1407
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Entity ID: 13
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50S ribosomal protein L17M [auth O]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplQMSMEG_1525MSMEI_1489
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Entity ID: 14
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50S ribosomal protein L18N [auth P]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplRMSMEG_1471
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Entity ID: 15
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50S ribosomal protein L19O [auth Q]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplSMSMEG_2440MSMEI_2379
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Entity ID: 16
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50S ribosomal protein L20P [auth R]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplTMSMEG_3791MSMEI_3703
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Entity ID: 17
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50S ribosomal protein L21Q [auth S]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplUMSMEG_4625MSMEI_4508
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Entity ID: 18
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50S ribosomal protein L22R [auth T]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplVMSMEG_1441MSMEI_1405
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Entity ID: 19
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50S ribosomal protein L23S [auth U]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplWMSMEG_1438MSMEI_1402
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Entity ID: 20
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50S ribosomal protein L24T [auth V]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplXMSMEG_1466MSMEI_1430
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Entity ID: 21
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50S ribosomal protein L25U [auth W]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplYctcMSMEG_5431
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Entity ID: 22
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50S ribosomal protein L27V [auth X]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmAMSMEG_4624MSMEI_4507
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Entity ID: 23
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50S ribosomal protein L28W [auth Y]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmBMSMEG_2400
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Entity ID: 24
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50S ribosomal protein L29X [auth Z]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmCMSMEG_1444MSMEI_1408
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth 1]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmDMSMEG_1473MSMEI_1437
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Entity ID: 28
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50S ribosomal protein L31BA [auth 2]75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmEMSMEG_4951MSMEI_4823
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Entity ID: 29
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50S ribosomal protein L32CA [auth 3]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmFMSMEG_5489MSMEI_5337
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Entity ID: 30
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50S ribosomal protein L33 1DA [auth 4]55Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmG1rpmG2MSMEG_1339MSMEI_1301
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Entity ID: 31
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50S ribosomal protein L34EA [auth 5]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmHMSMEG_6946MSMEI_6752
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Entity ID: 32
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50S ribosomal protein L35FA [auth 6]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmIMSMEG_3792MSMEI_3704
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Entity ID: 33
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50S ribosomal protein L36GA [auth 7]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmJMSMEG_1520MSMEI_1484
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein bL37HA [auth 8]24Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1916
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Entity ID: 25
MoleculeChainsLengthOrganismImage
P-tRNAfMetY [auth B]118Mycolicibacterium smegmatis MC2 155
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Entity ID: 26
MoleculeChainsLengthOrganismImage
23S rRNAZ [auth A]3120Mycolicibacterium smegmatis MC2 155
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release