4WRA

Complex of 70S ribosome with tRNA-Tyr and mRNA with A-A mismatch in the first position in the A-site and with antibiotic paromomycin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the translational infidelity mechanism.

Rozov, A.Demeshkina, N.Westhof, E.Yusupov, M.Yusupova, G.

(2015) Nat Commun 6: 7251-7251

  • DOI: 10.1038/ncomms8251
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The decoding of mRNA on the ribosome is the least accurate process during genetic information transfer. Here we propose a unified decoding mechanism based on 11 high-resolution X-ray structures of the 70S ribosome that explains the occurrence of miss ...

    The decoding of mRNA on the ribosome is the least accurate process during genetic information transfer. Here we propose a unified decoding mechanism based on 11 high-resolution X-ray structures of the 70S ribosome that explains the occurrence of missense errors during translation. We determined ribosome structures in rare states where incorrect tRNAs were incorporated into the peptidyl-tRNA-binding site. These structures show that in the codon-anticodon duplex, a G·U mismatch adopts the Watson-Crick geometry, indicating a shift in the tautomeric equilibrium or ionization of the nucleobase. Additional structures with mismatches in the 70S decoding centre show that the binding of any tRNA induces identical rearrangements in the centre, which favours either isosteric or close to the Watson-Crick geometry codon-anticodon pairs. Overall, the results suggest that a mismatch escapes discrimination by preserving the shape of a Watson-Crick pair and indicate that geometric selection via tautomerism or ionization dominates the translational infidelity mechanism.


    Organizational Affiliation

    Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg; CNRS, UMR7104; INSERM, U964, Illkirch 67400, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
1E, 12
256Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
2E, 22
239Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
3E, 32
209Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
4E, 42
162Thermus thermophilusMutation(s): 0 
Gene Names: rpsE (rps5)
Find proteins for P27152 (Thermus thermophilus)
Go to UniProtKB:  P27152
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
5E, 52
101Thermus thermophilusMutation(s): 0 
Gene Names: rpsF (rps6)
Find proteins for P23370 (Thermus thermophilus)
Go to UniProtKB:  P23370
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
6E, 62
156Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
7E, 72
138Thermus thermophilusMutation(s): 0 
Gene Names: rpsH (rps8)
Find proteins for P24319 (Thermus thermophilus)
Go to UniProtKB:  P24319
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
8E, 82
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: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
1I, 1A
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJ (rps10)
Find proteins for P80375 (Thermus thermophilus)
Go to UniProtKB:  P80375
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
2I, 2A
129Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
3I, 3A
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsL (rps12)
Find proteins for P17293 (Thermus thermophilus)
Go to UniProtKB:  P17293
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
4I, 4A
126Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
5I, 5A
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZ (rps14, rpsN)
Find proteins for P24320 (Thermus thermophilus)
Go to UniProtKB:  P24320
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
6I, 6A
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsO (rps15)
Find proteins for P80378 (Thermus thermophilus)
Go to UniProtKB:  P80378
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
7I, 7A
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
8I, 8A
105Thermus aquaticusMutation(s): 0 
Gene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
9I, 9A
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AI, AA
93Thermus thermophilusMutation(s): 0 
Gene Names: rpsS (rps19)
Find proteins for P80381 (Thermus thermophilus)
Go to UniProtKB:  P80381
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
BI, BA
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: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
1F, 1B
27Thermus thermophilusMutation(s): 0 
Gene Names: rpsU
Find proteins for P62612 (Thermus thermophilus)
Go to UniProtKB:  P62612
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
11, 19
276Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
21, 29
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
31, 39
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
41, 49
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
51, 59
180Thermus thermophilusMutation(s): 0 
Gene Names: rplF (rpl6)
Find proteins for P24316 (Thermus thermophilus)
Go to UniProtKB:  P24316
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
61, 69
148Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
58, 15
140Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
68, 25
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
78, 35
150Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
88, 45
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
98, 55
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
A8, 65
112Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
B8, 75
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
C8, 85
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60491
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
D8, 95
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
E8, A5
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
F8, B5
96Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
G8, C5
110Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
H8, D5
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
I8, E5
85Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
J8, F5
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
K8, G5
72Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP6
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
L8, H5
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
M8, I5
71Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJE1
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
N8, J5
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
P8, L5
49Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
Q8, M5
65Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKU1
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNA13,1G1522Thermus thermophilus HB8
Entity ID: 22
MoleculeChainsLengthOrganism
tRNA-Tyr1K85Escherichia coli
Entity ID: 23
MoleculeChainsLengthOrganism
tRNA-fMet2K,2L77Escherichia coli
Entity ID: 24
MoleculeChainsLengthOrganism
tRNA-Tyr3K,1L85Escherichia coli
Entity ID: 25
MoleculeChainsLengthOrganism
mRNA4K,4L30Thermus thermophilus HB8
Entity ID: 26
MoleculeChainsLengthOrganism
23S ribosomal RNA1H,142918Thermus thermophilus HB8
Entity ID: 27
MoleculeChainsLengthOrganism
5S ribosomal RNA16,1J122Thermus thermophilus HB8
Entity ID: 55
MoleculeChainsLengthOrganism
tRNA-Tyr3L85Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
32, 3E, 5A, 5I, C5, G8
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PAR
Query on PAR

Download SDF File 
Download CCD File 
13, 1G
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 
11, 13, 14, 16, 1G, 1H, 1J, 1K, 21, 25, 29, 2K, 2L, 31, 35, 39, 3E, 3I, 41, 45, 5E, 78, 85, 88, C5, I8, L5, L8, P8
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1K, 1L, 2K, 2L, 3K, 3L
RNA LINKINGC9 H13 N2 O9 PU
OMC
Query on OMC
2K, 2L
RNA LINKINGC10 H16 N3 O8 PC
4SU
Query on 4SU
2K, 2L
RNA LINKINGC9 H13 N2 O8 P SU
MIA
Query on MIA
1K, 3L
RNA LINKINGC16 H26 N5 O7 P SA
QUO
Query on QUO
1K
RNA LINKINGC17 H26 N5 O10 PG
5MU
Query on 5MU
1K, 2K, 2L
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 209.900α = 90.00
b = 450.900β = 90.00
c = 622.700γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Type: Database references