6NSH

Modified ASL proline bound to Thermus thermophilus 70S (near-cognate)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing.

Hoffer, E.Hong, S.Sunita, S.Maehigashi, T.Gonzalez Jnr, R.L.Whitford, P.Dunham, C.M.

(2020) Elife 9

  • DOI: 10.7554/eLife.51898
  • Primary Citation of Related Structures:  
    6O3M, 6NSH, 6NTA, 6NUO, 6NWY, 6OSI

  • PubMed Abstract: 
  • Modifications in the tRNA anticodon loop, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguanosine modification at ...

    Modifications in the tRNA anticodon loop, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguanosine modification at guanine nucleotide 37 (m 1 G37) located in the anticodon loop andimmediately adjacent to the anticodon nucleotides 34, 35, 36. The absence of m 1 G37 in tRNA Pro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNA Pro bound to either cognate or slippery codons to determine how the m 1 G37 modification prevents mRNA frameshifting. The structures reveal that certain codon-anticodon contexts and the lack of m 1 G37 destabilize interactions of tRNA Pro with the P site of the ribosome, causing large conformational changes typically only seen during EF-G-mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m 1 G37 stabilizes the interactions of tRNA Pro with the ribosome in the context of a slippery mRNA codon.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, United States.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2RDYD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3REYE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4RFYF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5RGYG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6RHYH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9RIYI148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13RNYN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14ROYO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 11
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50S ribosomal protein L15RPYP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 12
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50S ribosomal protein L16RQYQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17RRYR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 14
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50S ribosomal protein L18RSYS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19RTYT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20RUYU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21RVYV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22RWYW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 19
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50S ribosomal protein L23RXYX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 20
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50S ribosomal protein L24RYYY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25RZYZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27R0Y085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28R1Y198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29R2Y272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30R3Y360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31R4Y471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32R5Y560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33R6Y654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34R7Y749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35R8Y865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36R9Y937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2QBXB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3QCXC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4QDXD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5QEXE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6QFXF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 38
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30S ribosomal protein S7QGXG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8QHXH138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9QIXI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10QJXJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11QKXK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12QLXL132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 44
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30S ribosomal protein S13QMXM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 45
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30S ribosomal protein S14 type ZQNXN61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 46
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30S ribosomal protein S15QOXO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 47
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30S ribosomal protein S16QPXP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17QQXQ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 49
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30S ribosomal protein S18QRXR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19QSXS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20QTXT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxQUXU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S rRNARA, YA2915Thermus thermophilus HB8
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S rRNARB, YB122Thermus thermophilus HB8
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Entity ID: 32
MoleculeChainsLengthOrganismImage
16S rRNAQA, XA1521Thermus thermophilus HB8
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  • Entity ID: 53
    MoleculeChainsLengthOrganismImage
    P-site ASLProQV, XV17Escherichia coli
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    • Entity ID: 54
      MoleculeChainsLengthOrganismImage
      mRNAQX, XX19Escherichia coli
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SF4
      Query on SF4

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      QD, XD
      IRON/SULFUR CLUSTER
      Fe4 S4
      LJBDFODJNLIPKO-VKOJMFJBAC
       Ligand Interaction
      ZN
      Query on ZN

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      QN, R4, R5, R6, R9, RY, XN, Y4, Y5, Y6, Y9, YY
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

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      QA, QF, R0, R1, R5, R8, RA, RB, RE, RF, RN, RO, RP, RQ, RT, RX, XA, XE, XL, XQ, XS, Y0, Y1, Y5, Y7, Y8, YA, YB, YD, YE, YO, YP, YQ, YR
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.40 Å
      • R-Value Free: 0.237 
      • R-Value Work: 0.198 
      • R-Value Observed: 0.200 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 210.123α = 90
      b = 451.799β = 90
      c = 622.957γ = 90
      Software Package:
      Software NamePurpose
      XDSdata reduction
      XSCALEdata scaling
      PHENIXphasing
      Cootmodel building
      PHENIXrefinement
      PDB_EXTRACTdata extraction

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM093278
      National Science Foundation (NSF, United States)United StatesCHE 1808711

      Revision History 

      • Version 1.0: 2020-10-14
        Type: Initial release
      • Version 1.1: 2020-10-21
        Changes: Database references