1XMO

Crystal Structure of mnm5U34t6A37-tRNALysUUU Complexed with AAG-mRNA in the Decoding Center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The role of modifications in codon discrimination by tRNA(Lys)(UUU).

Murphy, F.V.Ramakrishnan, V.Malkiewicz, A.Agris, P.F.

(2004) Nat.Struct.Mol.Biol. 11: 1186-1191

  • DOI: 10.1038/nsmb861
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The natural modification of specific nucleosides in many tRNAs is essential during decoding of mRNA by the ribosome. For example, tRNA(Lys)(UUU) requires the modification N6-threonylcarbamoyladenosine at position 37 (t(6)A37), adjacent and 3' to the ...

    The natural modification of specific nucleosides in many tRNAs is essential during decoding of mRNA by the ribosome. For example, tRNA(Lys)(UUU) requires the modification N6-threonylcarbamoyladenosine at position 37 (t(6)A37), adjacent and 3' to the anticodon, to bind AAA in the A site of the ribosomal 30S subunit. Moreover, it can only bind both AAA and AAG lysine codons when doubly modified with t(6)A37 and either 5-methylaminomethyluridine or 2-thiouridine at the wobble position (mnm(5)U34 or s(2)U34). Here we report crystal structures of modified tRNA anticodon stem-loops bound to the 30S ribosomal subunit with lysine codons in the A site. These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
138Thermus aquaticusMutation(s): 0 
Gene Names: rpsH
Find proteins for A0A0M9AFS9 (Thermus aquaticus)
Go to UniProtKB:  A0A0M9AFS9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
N
61Thermus aquaticusMutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
105Thermus aquaticusMutation(s): 0 
Gene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
V
27Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1522Thermus thermophilus HB27
Entity ID: 2
MoleculeChainsLengthOrganism
A-Site Messenger RNAW3N/A
Entity ID: 3
MoleculeChainsLengthOrganism
Anticodon Transfer RNAX11N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PAR
Query on PAR

Download SDF File 
Download CCD File 
A
PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, J, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MNU
Query on MNU
X
RNA LINKINGC11 H18 N3 O9 PU
T6A
Query on T6A
X
RNA LINKINGC15 H21 N6 O11 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.231 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 400.811α = 90.00
b = 400.811β = 90.00
c = 176.125γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance