4V4X

Crystal structure of the 70S Thermus thermophilus ribosome showing how the 16S 3'-end mimicks mRNA E and P codons.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for messenger RNA movement on the ribosome.

Yusupova, G.Jenner, L.Rees, B.Moras, D.Yusupov, M.

(2006) Nature 444: 391-394

  • DOI: 10.1038/nature05281
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Translation initiation is a major determinant of the overall expression level of a gene. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read firs ...

    Translation initiation is a major determinant of the overall expression level of a gene. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read first and in the correct frame. Little is known about the molecular basis for the interaction of mRNA with the ribosome at different states of translation. Recent crystal structures of the ribosomal subunits, the empty 70S ribosome and the 70S ribosome containing functional ligands have provided information about the general organization of the ribosome and its functional centres. Here we compare the X-ray structures of eight ribosome complexes modelling the translation initiation, post-initiation and elongation states. In the initiation and post-initiation complexes, the presence of the Shine-Dalgarno (SD) duplex causes strong anchoring of the 5'-end of mRNA onto the platform of the 30S subunit, with numerous interactions between mRNA and the ribosome. Conversely, the 5' end of the 'elongator' mRNA lacking SD interactions is flexible, suggesting a different exit path for mRNA during elongation. After the initiation of translation, but while an SD interaction is still present, mRNA moves in the 3'-->5' direction with simultaneous clockwise rotation and lengthening of the SD duplex, bringing it into contact with ribosomal protein S2.


    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AE
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
AF
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
AG
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
AH
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
AI
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
AJ
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
AK
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
AL
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
AM
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
AN
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
AO
132Thermus 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
AP
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
AQ
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
AR
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
AS
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
AT
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsQ (rps17)
Find proteins for P24321 (Thermus thermophilus)
Go to UniProtKB:  P24321
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AU
88Thermus thermophilusMutation(s): 0 
Gene Names: rpsR (rps18)
Find proteins for P80382 (Thermus thermophilus)
Go to UniProtKB:  P80382
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AV
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
AW
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
AX
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: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
BC
229Thermus thermophilusMutation(s): 0 
Gene Names: rplA (rpl1)
Find proteins for P27150 (Thermus thermophilus)
Go to UniProtKB:  P27150
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD
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: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE
206Thermus thermophilusMutation(s): 0 
Gene Names: rplC (rpl3)
Find proteins for P52860 (Thermus thermophilus)
Go to UniProtKB:  P52860
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF
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: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG
182Thermus thermophilusMutation(s): 0 
Gene Names: rplE (rpl5)
Find proteins for P41201 (Thermus thermophilus)
Go to UniProtKB:  P41201
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH
180Thermus thermophilusMutation(s): 0 
Gene Names: rplF (rpl6)
Find proteins for P24316 (Thermus thermophilus)
Go to UniProtKB:  P24316
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BK
148Thermus thermophilusMutation(s): 0 
Gene Names: rplI (rpl9)
Find proteins for P27151 (Thermus thermophilus)
Go to UniProtKB:  P27151
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BL
147Thermus thermophilusMutation(s): 0 
Gene Names: rplK (rpl11)
Find proteins for P36238 (Thermus thermophilus)
Go to UniProtKB:  P36238
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BM
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
BN
122Thermus thermophilusMutation(s): 0 
Gene Names: rplN (rpl14)
Find proteins for P60558 (Thermus thermophilus)
Go to UniProtKB:  P60558
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BO
150Thermus thermophilusMutation(s): 0 
Gene Names: rplO (rpl15)
Find proteins for P74910 (Thermus thermophilus)
Go to UniProtKB:  P74910
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BP
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
BQ
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
BR
112Thermus thermophilusMutation(s): 0 
Gene Names: rplR (rpl18)
Find proteins for P80320 (Thermus thermophilus)
Go to UniProtKB:  P80320
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BS
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
BT
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
BU
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
BV
113Thermus thermophilusMutation(s): 0 
Gene Names: rplV (rpl22)
Find proteins for P48286 (Thermus thermophilus)
Go to UniProtKB:  P48286
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BW
96Thermus thermophilusMutation(s): 0 
Gene Names: rplW
Find proteins for Q9RA57 (Thermus thermophilus)
Go to UniProtKB:  Q9RA57
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BX
110Thermus thermophilusMutation(s): 0 
Gene Names: rplX (rpl24)
Find proteins for Q56435 (Thermus thermophilus)
Go to UniProtKB:  Q56435
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BY
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
BZ
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 L29
B1
67Thermus thermophilusMutation(s): 0 
Gene Names: rpmC (rpl29)
Find proteins for Q9LCY4 (Thermus thermophilus)
Go to UniProtKB:  Q9LCY4
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B2
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmD (rpl30)
Find proteins for P74909 (Thermus thermophilus)
Go to UniProtKB:  P74909
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B3
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: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B4
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: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B5
54Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B6
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
B7
65Thermus thermophilusMutation(s): 0 
Gene Names: rpmI (rpl35)
Find proteins for P80341 (Thermus thermophilus)
Go to UniProtKB:  P80341
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B8
37Thermus thermophilusMutation(s): 0 
Gene Names: rpmJ (rpl36)
Find proteins for P80256 (Thermus thermophilus)
Go to UniProtKB:  P80256
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAAA1522Thermus thermophilus HB8
Entity ID: 2
MoleculeChainsLengthOrganism
tRNA fMET (unmodified bases)AC77Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
tRNA PHE (unmodified bases)AD76Thermus thermophilus HB8
Entity ID: 24
MoleculeChainsLengthOrganism
23S ribosomal RNABA2916Thermus thermophilus HB8
Entity ID: 25
MoleculeChainsLengthOrganism
5S ribosomal RNABB123Thermus thermophilus HB8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.263 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 509.520α = 90.00
b = 509.520β = 90.00
c = 804.940γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2017-11-22
    Type: Refinement description