6DZI

Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 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

Zinc depletion induces ribosome hibernation in mycobacteria.

Li, Y.Sharma, M.R.Koripella, R.K.Yang, Y.Kaushal, P.S.Lin, Q.Wade, J.T.Gray, T.A.Derbyshire, K.M.Agrawal, R.K.Ojha, A.K.

(2018) Proc Natl Acad Sci U S A 115: 8191-8196

  • DOI: 10.1073/pnas.1804555115
  • Primary Citation of Related Structures:  
    6DZI, 6DZK, 6DZP

  • PubMed Abstract: 
  • Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc homeostasis are unknown. Here, we show that the C- ribosome in Mycobacterium smegmatis is the exclusive target of a bacterial protein Y homolog, referred to as mycobacterial-specific protein Y (MPY), which binds to the decoding region of the 30S subunit, thereby inactivating the ribosome ...

    Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc homeostasis are unknown. Here, we show that the C- ribosome in Mycobacterium smegmatis is the exclusive target of a bacterial protein Y homolog, referred to as mycobacterial-specific protein Y (MPY), which binds to the decoding region of the 30S subunit, thereby inactivating the ribosome. MPY binding is dependent on another mycobacterial protein, MPY recruitment factor (MRF), which is induced on zinc depletion, and interacts with C- ribosomes. MPY binding confers structural stability to C- ribosomes, promoting survival of growth-arrested cells under zinc-limiting conditions. Binding of MPY also has direct influence on the dynamics of aminoglycoside-binding pockets of the C- ribosome to inhibit binding of these antibiotics. Together, our data suggest that zinc limitation leads to ribosome hibernation and aminoglycoside resistance in mycobacteria. Furthermore, our observation of the expression of the proteins of C- ribosomes in Mycobacterium tuberculosis in a mouse model of infection suggests that ribosome hibernation could be relevant in our understanding of persistence and drug tolerance of the pathogen encountered during chemotherapy of TB.


    Organizational Affiliation

    Department of Biomedical Sciences, University at Albany, Albany, NY 12208.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CONSERVED PROTEIN DOMAINB [auth j]32Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth k]208Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsCMSMEG_1442MSMEI_1406
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth l]200Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsDMSMEG_1523MSMEI_1487
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth m]180Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsEMSMEG_1472MSMEI_1436
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth n]96Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: rpsFERS451418_06682
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Entity ID: 7
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30S ribosomal protein S7G [auth p]155Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsGMSMEG_1399MSMEI_1361
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Entity ID: 8
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30S ribosomal protein S8H [auth q]131Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsHMSMEG_1469MSMEI_1433
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Entity ID: 9
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30S ribosomal protein S9I [auth 4]126Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsIMSMEG_1557MSMEI_1520
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Entity ID: 10
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30S ribosomal protein S10J [auth s]99Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsJMSMEG_1435MSMEI_1399
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Entity ID: 11
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30S ribosomal protein S11K [auth t]115Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsKMSMEG_1522MSMEI_1486
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Entity ID: 12
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30S ribosomal protein S12L [auth u]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsLMSMEG_1398MSMEI_1360
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Entity ID: 13
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30S ribosomal protein S13M [auth v]116Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsMMSMEG_1521MSMEI_1485
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Entity ID: 14
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30S ribosomal protein S15N [auth x]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsOMSMEG_2654MSMEI_2591
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Entity ID: 15
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30S ribosomal protein S16O [auth z]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsPMSMEG_2435MSMEI_2374
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Entity ID: 16
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30S ribosomal protein S17P [auth 5]94Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsQMSMEG_1445MSMEI_1409
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Entity ID: 17
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30S ribosomal protein S19Q [auth 6]82Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsSMSMEG_1440MSMEI_1404
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Entity ID: 18
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30S ribosomal protein S20R [auth 7]85Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsTMSMEG_4571MSMEI_4459
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Entity ID: 19
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30S ribosomal protein S2S [auth 8]228Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsBMSMEG_2519MSMEI_2460
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Entity ID: 20
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30S ribosomal protein S18 1T [auth r]84Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsR1rpsR2MSMEG_6065MSMEI_5905
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome hibernation promoting factorU [auth Y]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: hpfMSMEG_1878
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Entity ID: 22
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30S ribosomal protein S14V [auth 9]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsNMSMEG_6066MSMEI_5906
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth C]275Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplBMSMEG_1439MSMEI_1403
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth D]214Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplCMSMEG_1436MSMEI_1400
UniProt
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Entity ID: 27
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50S ribosomal protein L4AA [auth E]209Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplDMSMEG_1437MSMEI_1401
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth F]182Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplEMSMEG_1467MSMEI_1431
UniProt
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Entity ID: 29
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50S ribosomal protein L6CA [auth G]176Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplFMSMEG_1470MSMEI_1434
UniProt
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Entity ID: 30
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50S ribosomal protein L9DA [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplIMSMEG_6894MSMEI_6710
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Entity ID: 31
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50S ribosomal protein L10EA [auth I]126Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplJMSMEG_1364MSMEI_1325
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Entity ID: 32
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50S ribosomal protein L11FA [auth J]133Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplKMSMEG_1346MSMEI_1308
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Entity ID: 33
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50S ribosomal protein L13GA [auth K]146Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplMMSMEG_1556MSMEI_1519
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Entity ID: 34
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50S ribosomal protein L14HA [auth L]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplNMSMEG_1465MSMEI_1429
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15IA [auth M]145Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplOMSMEI_1438
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Entity ID: 36
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50S ribosomal protein L16JA [auth N]136Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplPMSMEG_1443MSMEI_1407
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Entity ID: 37
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50S ribosomal protein L17KA [auth O]118Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplQMSMEG_1525MSMEI_1489
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Entity ID: 38
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50S ribosomal protein L18LA [auth P]126Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplRMSMEI_1435
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Entity ID: 39
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50S ribosomal protein L19MA [auth Q]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplSMSMEG_2440MSMEI_2379
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Entity ID: 40
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50S ribosomal protein L20NA [auth R]124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplTMSMEG_3791MSMEI_3703
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Entity ID: 41
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50S ribosomal protein L21OA [auth S]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplUMSMEG_4625MSMEI_4508
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Entity ID: 42
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50S ribosomal protein L22PA [auth T]114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplVMSMEG_1441MSMEI_1405
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Entity ID: 43
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50S ribosomal protein L23QA [auth U]97Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplWMSMEG_1438MSMEI_1402
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Entity ID: 44
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50S ribosomal protein L24RA [auth V]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplXMSMEG_1466MSMEI_1430
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Entity ID: 45
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50S ribosomal protein L25SA [auth W]192Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplYctcMSMEG_5431
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Entity ID: 46
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50S ribosomal protein L27TA [auth X]79Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmAMSMEG_4624MSMEI_4507
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Entity ID: 47
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50S ribosomal protein L29UA [auth Z]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmCMSMEG_1444MSMEI_1408
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30VA [auth a]59Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmDMSMEG_1473MSMEI_1437
UniProt
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32WA [auth b]54Mycolicibacterium 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: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 2XA [auth c]53Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmG2MSMEG_6067MSMEI_5907
UniProt
Find proteins for A0R551 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34YA [auth d]46Mycolicibacterium 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: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35ZA [auth e]63Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmIMSMEG_3792MSMEI_3704
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Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36AB [auth f]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: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31BB [auth g]82Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmEMSMEG_6070
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28CB [auth y]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinDB [auth 3]23Mycolicibacterium 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 h]1511Mycolicibacterium smegmatis MC2 155
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Entity ID: 23
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23 S rRNA (3119-MER)W [auth A]3119Mycolicibacterium smegmatis MC2 155
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Entity ID: 24
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5S RNA (118-MER)X [auth B]118Mycolicibacterium smegmatis MC2 155
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM061576
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI107595
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI097191

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence