6MPF

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a 2-thiocytidine (s2C32) and inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 1 (TRNAARG1) bound to an mRNA with an CGC-codon in the A-site and paromomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.

Vangaveti, S.Cantara, W.A.Spears, J.L.DeMirci, H.Murphy IV, F.V.Ranganathan, S.V.Sarachan, K.L.Agris, P.F.

(2020) J Mol Biol 432: 913-929

  • DOI: 10.1016/j.jmb.2019.12.016
  • Primary Citation of Related Structures:  
    6DTI, 6MKN, 6MPF, 6MPI

  • PubMed Abstract: 
  • Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA Arg isoacceptors. The anticodon stem and loop (ASL) domains of tRNA Arg1 and tRNA Arg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I 34 ) and 37 (m 2 A 37 ) ...

    Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA Arg isoacceptors. The anticodon stem and loop (ASL) domains of tRNA Arg1 and tRNA Arg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I 34 ) and 37 (m 2 A 37 ). tRNA Arg1 is also modified from cytidine to 2-thiocytidine at position 32 (s 2 C 32 ). The s 2 C 32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s 2 C 32 for C 32 in the Saccharomyces cerevisiae tRNA Ile IAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s 2 C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASL Arg1 ICG and ASL Arg2 ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C 32- A 38 cross-loop interaction but failed to fully explain the means by which s 2 C 32 restricts I 34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C 32- A 38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.


    Organizational Affiliation

    Department of Biological Sciences, University at Albany-SUNY, 1400 Washington Ave., Albany, NY, 12222, USA; The RNA Institute, University at Albany-SUNY, 1400 Washington Ave., Albany, NY, 12222, USA. Electronic address: paul.agris@duke.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B234Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
UniProt
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UniProt GroupP80371
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L124Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M125Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P83Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R73Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S80Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth V]24Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1,508Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
mRNA A-site fragmentV [auth W]4Escherichia coli
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Entity ID: 23
MoleculeChainsLengthOrganismImage
tRNA ASL Escherichia coli Arg1W [auth X]11Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
X [auth A]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
SD [auth D],
WD [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
BA [auth A],
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth E],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth J],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth J],
WA [auth A],
WB [auth A],
WC [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth W],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth X],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 402.33α = 90
b = 402.33β = 90
c = 176.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2RO1GM23037-25
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM110588-01
National Science Foundation (NSF, United States)United StatesMCB1101859
National Science Foundation (NSF, United States)United StatesCHE1407042

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 2.0: 2020-01-29
    Changes: Data collection, Database references, Polymer sequence
  • Version 2.1: 2020-03-11
    Changes: Database references