ISDA

Entry Detail

PDB ID:

4V4P

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

Thermus thermophilus

PDB Version:

Deposition Date:

2005-01-19

Release Date:

2014-07-09

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

5.50 Å

R-Value Free:

0.35

R-Value Work:

0.30

R-Value Observed:

0.30

Space Group:

I 4 2 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:Y (auth: A0)
Chain Length:118
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:Z (auth: A1)
Chain Length:118
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:AA (auth: A2)
Chain Length:100
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:BA (auth: A3)
Chain Length:91
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:CA (auth: A4)
Chain Length:73
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:DA (auth: A5)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:EA (auth: A6)
Chain Length:82
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:FA (auth: A7)
Chain Length:47
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:GA (auth: A8)
Chain Length:64
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:HA (auth: A9)
Chain Length:36
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:B (auth: AA)
Chain Length:2915
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:A (auth: AB)
Chain Length:123
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L1
Chain IDs:C (auth: AC)
Chain Length:228
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P27150 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:D (auth: AD)
Chain Length:178
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:E (auth: AE)
Chain Length:338
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:F (auth: AF)
Chain Length:246
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:G (auth: AG)
Chain Length:176
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:H (auth: AH)
Chain Length:177
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L7/L12
Chain IDs:I (auth: AI), J (auth: AJ)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:K (auth: AK)
Chain Length:149
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L11
Chain IDs:L (auth: AL)
Chain Length:141
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:M (auth: AM)
Chain Length:145
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:N (auth: AN)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:O (auth: AO)
Chain Length:164
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:P (auth: AP)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:Q (auth: AQ)
Chain Length:186
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:R (auth: AR)
Chain Length:66
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:S (auth: AS)
Chain Length:113
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP3 Pfam ID:PF00237

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:T (auth: AT)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:U (auth: AU)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S general stress protein CTC (L25)
Chain IDs:V (auth: AV)
Chain Length:253
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:W (auth: AW)
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:X (auth: AX)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Polymer Type:polyribonucleotide
Description:thrS mRNA operator
Chain IDs:LA (auth: B1)
Chain Length:78
Number of Molecules:1
Biological Source:

Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:IA (auth: BA)
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Description:tRNA Phe (unmodified bases)
Chain IDs:JA (auth: BB), KA (auth: BC)
Chain Length:76
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:MA (auth: BE)
Chain Length:256
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:NA (auth: BF)
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:OA (auth: BG)
Chain Length:209
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:PA (auth: BH)
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:QA (auth: BI)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:RA (auth: BJ)
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P17291 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:SA (auth: BK)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:TA (auth: BL)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:UA (auth: BM)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:VA (auth: BN)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:WA (auth: BO)
Chain Length:135
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:XA (auth: BP)
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80377 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:YA (auth: BQ)
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:ZA (auth: BR)
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:AB (auth: BS)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJH3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:BB (auth: BT)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:CB (auth: BU)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:DB (auth: BV)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:EB (auth: BW)
Chain Length:106
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein Thx
Chain IDs:FB (auth: BX)
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Ligand Molecules

Primary Citation

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.Show

Science 308 120 123 (2005)

PMID: 15802605 DOI: 10.1126/science.1105639

Abstact

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.

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Primary Citation of related structures