6OF6

Crystal structure of tRNA^ Ala(GGC) bound to cognate 70S A-site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Disruption of evolutionarily correlated tRNA elements impairs accurate decoding.

Nguyen, H.A.Sunita, S.Dunham, C.M.

(2020) Proc Natl Acad Sci U S A 117: 16333-16338

  • DOI: 10.1073/pnas.2004170117
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide se ...

    Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem-loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. The molecular basis for how these two tRNA features combine to ensure accurate decoding is unclear. Here, we solved structures of the bacterial ribosome containing either wild-type [Formula: see text] or [Formula: see text] containing a reversed 32-38 pair on cognate and near-cognate codons. Structures of wild-type [Formula: see text] bound to the ribosome reveal 23S ribosomal RNA (rRNA) nucleotide A1913 positional changes that are dependent on whether the codon-anticodon interaction is cognate or near cognate. Further, the 32-38 pair is destabilized in the context of a near-cognate codon-anticodon pair. Reversal of the pairing in [Formula: see text] ablates A1913 movement regardless of whether the interaction is cognate or near cognate. These results demonstrate that disrupting 32-38 and anticodon sequences alters interactions with the ribosome that directly contribute to misreading.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322; christine.m.dunham@emory.edu.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4QD, XD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6QF, XF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7QG, XG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9QI, XI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11QK, XK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12QL, XL131Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13QM, XM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15QO, XO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16QP, XP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17QQ, XQ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20QT, XT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27R0, Y085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28R1, Y198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30R3, Y360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31R4, Y471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32R5, Y560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33R6, Y654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34R7, Y749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35R8, Y865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2RD, YD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3RE, YE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4RF, YF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5RG, YG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6RH, YH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9RI, YI148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13RN, YN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15RP, YP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17RR, YR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18RS, YS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19RT, YT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20RU, YU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23RX, YX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24RY, YY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25RZ, YZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10QJ, XJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type ZQN, XN61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18QR, XR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19QS, XS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2QB, XB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein ThxQU, XU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29R2, Y272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3QC, XC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36R9, Y937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14RO, YO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16RQ, YQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5QE, XE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21RV, YV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22RW, YW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8QH, XH138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAQA, XA1522Thermus thermophilus HB8

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Entity ID: 23
MoleculeChainsLengthOrganism
E-site tRNAAla(GGC)QW, XW76Escherichia coli

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Entity ID: 25
MoleculeChainsLengthOrganism
A-site tRNAAla(GGC)QY, XY76Escherichia coli #1/H766

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Entity ID: 37
MoleculeChainsLengthOrganism
5S rRNARB, YB122Thermus thermophilus HB8

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Entity ID: 22
MoleculeChainsLengthOrganism
P-site tRNAfMetQV, XV77Escherichia coli
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Entity ID: 24
MoleculeChainsLengthOrganism
mRNAQX, XX19Escherichia coli

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Entity ID: 36
MoleculeChainsLengthOrganism
23S rRNARA, YA2915Thermus thermophilus HB8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

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QA, XA
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
SF4
Query on SF4

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

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QY
ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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QN, XN
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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QA, QD, QF, QH, QK, QL, QM, QV, QX, R0, R1, R5, R8, R9, RA, RB, RD, RE, RF, RG, RI, RP, RR, RT, XA, XB, XD, XF, XJ, XK, XL, XM, XV, XX, Y0, Y2, Y3, Y4, Y5, Y7, Y8, YA, YB, YD, YE, YF, YG, YH, YI, YN, YO, YP, YQ, YR, YT, YU, YV, YW, YX, YY
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.26α = 90
b = 452.33β = 90
c = 626.52γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

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 StatesR01 GM093278
National Science Foundation (NSF, United States)United StatesCHE 1808711

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2020-07-15
    Changes: Database references
  • Version 1.3: 2020-07-29
    Changes: Database references, Derived calculations