5ZEB

M. Smegmatis P/P state 70S ribosome structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth c]275Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsCMSMEG_1442MSMEI_1406
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Entity ID: 3
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30S ribosomal protein S5C [auth e]214Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsEMSMEG_1472MSMEI_1436
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7D [auth g]156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsGMSMEG_1399MSMEI_1361
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8E [auth h]132Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsHMSMEG_1469MSMEI_1433
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Entity ID: 6
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30S ribosomal protein S9F [auth i]150Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsIMSMEG_1557MSMEI_1520
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Entity ID: 7
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30S ribosomal protein S10G [auth j]101Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsJMSMEG_1435MSMEI_1399
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Entity ID: 8
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30S ribosomal protein S11H [auth k]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsKMSMEG_1522MSMEI_1486
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Entity ID: 9
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30S ribosomal protein S12I [auth l]124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsLMSMEG_1398MSMEI_1360
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Entity ID: 10
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30S ribosomal protein S15J [auth o]89Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsOMSMEG_2654MSMEI_2591
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Entity ID: 11
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30S ribosomal protein S17K [auth q]98Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsQMSMEG_1445MSMEI_1409
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Entity ID: 12
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30S ribosomal protein S18 2L [auth r]84Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsR2rpsR1MSMEG_6895MSMEI_6711
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Entity ID: 13
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30S ribosomal protein S19M [auth s]93Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsSMSMEG_1440MSMEI_1404
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Entity ID: 14
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30S ribosomal protein S20N [auth t]86Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsTMSMEG_4571MSMEI_4459
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Entity ID: 16
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30S ribosomal protein S14 type ZP [auth n]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsZrpsNMSMEG_1468MSMEI_1432
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Entity ID: 17
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30S ribosomal protein S2Q [auth b]277Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsBMSMEG_2519MSMEI_2460
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Entity ID: 18
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30S ribosomal protein S4R [auth d]201Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsDMSMEG_1523MSMEI_1487
UniProt
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Entity ID: 19
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30S ribosomal protein S6S [auth f]96Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 20
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30S ribosomal protein S13T [auth m]124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsMMSMEG_1521MSMEI_1485
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Entity ID: 21
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30S ribosomal protein S16U [auth p]156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsPMSMEG_2435MSMEI_2374
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Entity ID: 22
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Conserved domain proteinV [auth u]33Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0945
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Entity ID: 23
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50S ribosomal protein L2W [auth C]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplBMSMEG_1439MSMEI_1403
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Entity ID: 24
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50S ribosomal protein L3X [auth D]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplCMSMEG_1436MSMEI_1400
UniProt
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Entity ID: 25
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50S ribosomal protein L4Y [auth E]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplDMSMEG_1437MSMEI_1401
UniProt
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Entity ID: 26
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50S ribosomal protein L5Z [auth F]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplEMSMEG_1467MSMEI_1431
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6AA [auth G]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplFMSMEG_1470MSMEI_1434
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Entity ID: 28
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50S ribosomal protein L9BA [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplIMSMEG_6894MSMEI_6710
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Entity ID: 29
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50S ribosomal protein L10CA [auth I]175Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplJMSMEG_1364MSMEI_1325
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Entity ID: 30
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50S ribosomal protein L11DA [auth J]142Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplKMSMEG_1346MSMEI_1308
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Entity ID: 31
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50S ribosomal protein L13EA [auth K]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplMMSMEG_1556MSMEI_1519
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Entity ID: 32
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50S ribosomal protein L14FA [auth L]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplNMSMEG_1465MSMEI_1429
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15GA [auth M]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplOMSMEG_1474
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Entity ID: 34
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50S ribosomal protein L16HA [auth N]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplPMSMEG_1443MSMEI_1407
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Entity ID: 35
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50S ribosomal protein L17IA [auth O]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplQMSMEG_1525MSMEI_1489
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Entity ID: 36
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50S ribosomal protein L18JA [auth P]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplRMSMEG_1471
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Entity ID: 37
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50S ribosomal protein L19KA [auth Q]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplSMSMEG_2440MSMEI_2379
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Entity ID: 38
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50S ribosomal protein L20LA [auth R]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplTMSMEG_3791MSMEI_3703
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Entity ID: 39
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50S ribosomal protein L21MA [auth S]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplUMSMEG_4625MSMEI_4508
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Entity ID: 40
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50S ribosomal protein L22NA [auth T]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplVMSMEG_1441MSMEI_1405
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Entity ID: 41
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50S ribosomal protein L23OA [auth U]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplWMSMEG_1438MSMEI_1402
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Entity ID: 42
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50S ribosomal protein L24PA [auth V]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplXMSMEG_1466MSMEI_1430
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Entity ID: 43
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50S ribosomal protein L25QA [auth W]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplYctcMSMEG_5431
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Entity ID: 44
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50S ribosomal protein L27RA [auth X]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmAMSMEG_4624MSMEI_4507
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Entity ID: 45
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50S ribosomal protein L28SA [auth Y]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmBMSMEG_2400
UniProt
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Entity ID: 46
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50S ribosomal protein L29TA [auth Z]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmCMSMEG_1444MSMEI_1408
UniProt
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Entity ID: 49
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50S ribosomal protein L30WA [auth 1]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmDMSMEG_1473MSMEI_1437
UniProt
Find proteins for A0QSG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31XA [auth 2]75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmEMSMEG_4951MSMEI_4823
UniProt
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32YA [auth 3]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmFMSMEG_5489MSMEI_5337
UniProt
Find proteins for A0R3I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 1ZA [auth 4]55Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmG1rpmG2MSMEG_1339MSMEI_1301
UniProt
Find proteins for A0QS39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth 5]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmHMSMEG_6946MSMEI_6752
UniProt
Find proteins for A0R7K0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth 6]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmIMSMEG_3792MSMEI_3704
UniProt
Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth 7]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmJMSMEG_1520MSMEI_1484
UniProt
Find proteins for A0QSL4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein bL37DB [auth 8]24Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1916
UniProt
Find proteins for A0QTP4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA [auth a]1528Mycolicibacterium smegmatis MC2 155
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Entity ID: 15
MoleculeChainsLengthOrganismImage
P-tRNAfMetO [auth v]77Escherichia coli
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Entity ID: 47
MoleculeChainsLengthOrganismImage
5S rRNAUA [auth B]118Mycolicibacterium smegmatis MC2 155
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Entity ID: 48
MoleculeChainsLengthOrganismImage
23S rRNAVA [auth A]3120Mycolicibacterium smegmatis MC2 155
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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