4V4P

Crystal structure of 70S ribosome with thrS operator and tRNAs.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.307 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding.

Jenner, L.Romby, P.Rees, B.Schulze-Briese, C.Springer, M.Ehresmann, C.Ehresmann, B.Moras, D.Yusupova, G.Yusupov, M.

(2005) Science 308: 120-123

  • DOI: 10.1126/science.1105639
  • Primary Citation of Related Structures:  1YL4, 1YL3

  • PubMed Abstract: 
  • The ribosome of Thermus thermophilus was cocrystallized with initiator transfer RNA (tRNA) and a structured messenger RNA (mRNA) carrying a translational operator. The path of the mRNA was defined at 5.5 angstroms resolution by comparing it with eith ...

    The ribosome of Thermus thermophilus was cocrystallized with initiator transfer RNA (tRNA) and a structured messenger RNA (mRNA) carrying a translational operator. The path of the mRNA was defined at 5.5 angstroms resolution by comparing it with either the crystal structure of the same ribosomal complex lacking mRNA or with an unstructured mRNA. A precise ribosomal environment positions the operator stem-loop structure perpendicular to the surface of the ribosome on the platform of the 30S subunit. The binding of the operator and of the initiator tRNA occurs on the ribosome with an unoccupied tRNA exit site, which is expected for an initiation complex. The positioning of the regulatory domain of the operator relative to the ribosome elucidates the molecular mechanism by which the bound repressor switches off translation. Our data suggest a general way in which mRNA control elements must be placed on the ribosome to perform their regulatory task.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
AC
228Thermus thermophilusGene Names: rplA (rpl1)
Find proteins for P27150 (Thermus thermophilus)
Go to UniProtKB:  P27150
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AD
178Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AE
338N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AF
246N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AG
176N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AH
177N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
AI, AJ
128N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
AK
149N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
AL
141N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AM
145N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AN
122N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AO
164N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AP
138N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AQ
186N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AR
66N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AS
113Thermus thermophilusGene Names: rplV (rpl22)
Find proteins for P48286 (Thermus thermophilus)
Go to UniProtKB:  P48286
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AT
84N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AU
119N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S general stress protein CTC (L25)
AV
253N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
AW
70N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
AX
60Thermus thermophilusGene Names: rpmD (rpl30)
Find proteins for P74909 (Thermus thermophilus)
Go to UniProtKB:  P74909
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
A0
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
A1
118N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
A2
100N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
A3
91N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
A4
73N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
A5
60N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A6
82N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
A7
47N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
A8
64N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
A9
36N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
BE
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
BF
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
BG
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
BH
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
BI
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
BJ
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
BK
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
BL
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
BM
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
BN
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
BO
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
BP
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
BQ
61Thermus aquaticusGene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
BR
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
BS
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
BT
105Thermus aquaticusGene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
BU
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
BV
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
BW
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
BX
27Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 1
MoleculeChainsLengthOrganism
5S ribosomal RNAAB123Thermus thermophilus HB8
Entity ID: 2
MoleculeChainsLengthOrganism
23S ribosomal RNAAA2915Thermus thermophilus HB8
Entity ID: 34
MoleculeChainsLengthOrganism
16S rRNABA1522Thermus thermophilus HB8
Entity ID: 35
MoleculeChainsLengthOrganism
tRNA Phe (unmodified bases)BB,BC76Thermus thermophilus HB8
Entity ID: 36
MoleculeChainsLengthOrganism
thrS mRNA operatorB178N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.307 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 508.640α = 90.00
b = 508.640β = 90.00
c = 806.250γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
CNSphasing

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