5ZLU

Ribosome Structure bound to ABC-F protein.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Ribosome protection by antibiotic resistance ATP-binding cassette protein.

Su, W., Kumar, V., Ding, Y., Ero, R., Serra, A., Lee, B.S.T., Wong, A.S.W., Shi, J., Sze, S.K., Yang, L., Gao, Y.G.

(2018) Proc Natl Acad Sci U S A 115: 5157-5162

  • DOI: 10.1073/pnas.1803313115
  • Primary Citation of Related Structures:  
    5ZLU

  • PubMed Abstract: 

    • The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer resistance to ribosome-targeting antibiotics through a yet unknown mechanism ...

    The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer resistance to ribosome-targeting antibiotics through a yet unknown mechanism. Among them, MsrE has been implicated in macrolide resistance. Here, we report the cryo-EM structure of ATP form MsrE bound to the ribosome. Unlike previously characterized ribosomal protection proteins, MsrE is shown to bind to ribosomal exit site. Our structure reveals that the domain linker forms a unique needle-like arrangement with two crossed helices connected by an extended loop projecting into the peptidyl-transferase center and the nascent peptide exit tunnel, where numerous antibiotics bind. In combination with biochemical assays, our structure provides insight into how MsrE binding leads to conformational changes, which results in the release of the drug. This mechanism appears to be universal for the ABC-F type ribosome protection proteins.

    Organizational Affiliation: 

    Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17B [auth A]104Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
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30S ribosomal protein S18C [auth B]73Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20D [auth C]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsT, rps20, TTHA1397
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19E [auth D]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsS, TTHA1688
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10F [auth E]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJ, TTHA1693
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxG [auth F]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsU, TTHA1396
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Entity ID: 9
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30S ribosomal protein S2I [auth H]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsB, rps2, TTHA0861
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Entity ID: 10
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30S ribosomal protein S3J [auth I]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsC, rps3, TTHA1686
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Entity ID: 11
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30S ribosomal protein S4K [auth J]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsD, rps4, TTHA1665
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Entity ID: 12
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30S ribosomal protein S5L [auth K]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsE, TTHA1675
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Entity ID: 13
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30S ribosomal protein S6M [auth L]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsF, TTHA0245
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Entity ID: 14
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30S ribosomal protein S7N [auth M]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsG, rps7, TTHA1696
UniProt
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Entity ID: 15
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30S ribosomal protein S8O [auth N]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsH, TTHA1678
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Entity ID: 16
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30S ribosomal protein S9P [auth O]128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsI, rps9, TTHA1464
UniProt
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Entity ID: 17
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30S ribosomal protein S11Q [auth P]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsK, rps11, TTHA1666
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Entity ID: 18
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30S ribosomal protein S12R [auth Q]132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsL, TTHA1697
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Entity ID: 19
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30S ribosomal protein S13S [auth R]126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsM, rps13, TTHA1667
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30S ribosomal protein S14 type ZT [auth S]61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZ, rpsN, TTHA1679
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Entity ID: 21
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30S ribosomal protein S15U [auth T]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsO, TTHA1138
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Entity ID: 22
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30S ribosomal protein S16V [auth U]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsP, TTHA1035
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Entity ID: 25
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50S ribosomal protein L1Y229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L2Z276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplB, TTHA1689
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Entity ID: 27
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50S ribosomal protein L3AA [auth a]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplC, TTHA1692
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Entity ID: 28
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50S ribosomal protein L4BA [auth b]210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplD, TTHA1691
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50S ribosomal protein L5CA [auth c]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplE, TTHA1680
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50S ribosomal protein L6DA [auth d]180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplF, TTHA1677
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50S ribosomal protein L10EA [auth e]173Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplJ, TTHA0209
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Entity ID: 32
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50S ribosomal protein L11FA [auth f]147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplK, TTHA0247
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Entity ID: 33
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50S ribosomal protein L13GA [auth g]140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplM, TTHA1465
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50S ribosomal protein L14HA [auth h]122Thermus thermophilus HB8Mutation(s): 0 
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50S ribosomal protein L15IA [auth i]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplO, TTHA1673
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50S ribosomal protein L16JA [auth j]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplP, TTHA1685
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50S ribosomal protein L17KA [auth k]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQ, rpl17, TTHA1663
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50S ribosomal protein L18LA [auth l]112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplR, TTHA1676
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50S ribosomal protein L19MA [auth m]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplS, TTHA1031
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50S ribosomal protein L20NA [auth n]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplT, TTHA0553
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50S ribosomal protein L21OA [auth o]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplU, TTHA1783
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50S ribosomal protein L22PA [auth p]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplV, TTHA1687
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50S ribosomal protein L23QA [auth q]96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplW, TTHA1690
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50S ribosomal protein L24RA [auth r]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplX, TTHA1681
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25SA [auth s]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplY, rpl25, rptL5, TTHA1589
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Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 46
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50S ribosomal protein L27TA [auth t]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmA, TTHA1782
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Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 47
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50S ribosomal protein L29UA [auth u]67Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
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50S ribosomal protein L30VA [auth v]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmD, TTHA1674
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Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31CB [auth CC],
WA [auth w]		71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmE, TTHA1073
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Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 50
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50S ribosomal protein L32XA [auth x]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmF, rpl32, TTHA0418
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Entity ID: 51
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50S ribosomal protein L33YA [auth y]54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmG, rpl33, TTHA0250
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
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50S ribosomal protein L34ZA [auth z]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmH, rpl34, TTHA0446
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Entity ID: 53
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50S ribosomal protein L35AB [auth AA]65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmI, TTHA0552
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Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
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50S ribosomal protein L36BB37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJ, TTHA1668
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Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Macrolide efflux proteinEB [auth EE]497Pseudomonas aeruginosaMutation(s): 0 
Gene Names: mel
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Find proteins for A0A1I9WCL8 (Pseudomonas aeruginosa)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (25-mer)A [auth W]25Thermus thermophilus HB8
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Entity ID: 8
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16S ribosomal RNAH [auth G]1,514Thermus thermophilus HB8
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Entity ID: 23
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23S ribosomal RNAW [auth V]2,875Thermus thermophilus HB8
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Entity ID: 24
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5S ribosomal RNAX123Thermus thermophilus HB8
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Entity ID: 55
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P-site tRNADB [auth DD]77Thermus thermophilus HB8
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
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HB [auth EE],
IB [auth EE]		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
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FB [auth Z],
GB [auth i]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIX

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)SingaporeMOE2014-T2-1-083

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Other, Refinement description
  • Version 1.2: 2019-11-06
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.3: 2019-12-04
    Changes: Advisory, Derived calculations