ISDA

Entry Detail

PDB ID:

4V51

Keywords:

RIBOSOME

Title:

Structure of the Thermus thermophilus 70S ribosome complexed with mRNA, tRNA and paromomycin

Biological Source:

Source Organism:

Escherichia coli K-12 , synthetic construct, THERMUS THERMOPHILUS

PDB Version:

Deposition Date:

2006-07-31

Release Date:

2014-07-09

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.80 Å

R-Value Free:

0.31

R-Value Work:

0.27

R-Value Observed:

0.27

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:A (auth: AA), EB (auth: CA)
Chain Length:1522
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S2
Chain IDs:B (auth: AB), FB (auth: CB)
Chain Length:256
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S3
Chain IDs:C (auth: AC), GB (auth: CC)
Chain Length:239
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S4
Chain IDs:D (auth: AD), HB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S5
Chain IDs:E (auth: AE), IB (auth: CE)
Chain Length:162
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S6
Chain IDs:F (auth: AF), JB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S7
Chain IDs:G (auth: AG), KB (auth: CG)
Chain Length:156
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P17291 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S8
Chain IDs:H (auth: AH), LB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S9
Chain IDs:I (auth: AI), MB (auth: CI)
Chain Length:128
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P62669 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S10
Chain IDs:J (auth: AJ), NB (auth: CJ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S11
Chain IDs:K (auth: AK), OB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S12
Chain IDs:L (auth: AL), PB (auth: CL)
Chain Length:135
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S13
Chain IDs:M (auth: AM), QB (auth: CM)
Chain Length:126
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80377 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S14
Chain IDs:N (auth: AN), RB (auth: CN)
Chain Length:61
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S15
Chain IDs:O (auth: AO), SB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S16
Chain IDs:P (auth: AP), TB (auth: CP)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJH3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q (auth: AQ), UB (auth: CQ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S18
Chain IDs:R (auth: AR), VB (auth: CR)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S19
Chain IDs:S (auth: AS), WB (auth: CS)
Chain Length:93
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S20
Chain IDs:T (auth: AT), XB (auth: CT)
Chain Length:106
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN THX
Chain IDs:U (auth: AU), YB (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Description:P-SITE TRNA FMET (UNMODIFIED BASES EXCEPT FOR THYMINE 54)
Chain IDs:V (auth: AV), ZB (auth: CV)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli K-12

Polymer Type:polyribonucleotide
Description:E-SITE TRNA PHE OR A-SITE TRNA PHE (UNMODIFIED BASES)
Chain IDs:W (auth: AW), Y (auth: AY), AC (auth: CW), CC (auth: CY)
Chain Length:76
Number of Molecules:4
Biological Source:Escherichia coli K-12

Polymer Type:polyribonucleotide
Description:MRNA
Chain IDs:X (auth: AX), BC (auth: CX)
Chain Length:24
Number of Molecules:2
Biological Source:synthetic construct

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L27
Chain IDs:Z (auth: B0), DC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60493 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L28
Chain IDs:AA (auth: B1), EC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60494 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L29
Chain IDs:BA (auth: B2), FC (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L30
Chain IDs:CA (auth: B3), GC (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L31
Chain IDs:DA (auth: B4), HC (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJE1 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L32
Chain IDs:EA (auth: B5), IC (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80339 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L33
Chain IDs:FA (auth: B6), JC (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P35871 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L34
Chain IDs:GA (auth: B7), KC (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80340 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L35
Chain IDs:HA (auth: B8), LC (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SKU1 Pfam ID:PF01632

Polymer Type:polyribonucleotide
Description:23S RIBOSOMAL RNA
Chain IDs:IA (auth: BA), MC (auth: DA)
Chain Length:2787
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Polymer Type:polyribonucleotide
Description:5S RIBOSOMAL RNA
Chain IDs:JA (auth: BB), NC (auth: DB)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L1
Chain IDs:KA (auth: BC), OC (auth: DC)
Chain Length:229
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP7 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L2
Chain IDs:LA (auth: BD), PC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L3
Chain IDs:MA (auth: BE), QC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN8 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L4
Chain IDs:NA (auth: BF), RC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN9 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L5
Chain IDs:OA (auth: BG), SC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L6
Chain IDs:PA (auth: BH), TC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L9
Chain IDs:QA (auth: BI), UC (auth: DI)
Chain Length:148
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L13
Chain IDs:RA (auth: BN), VC (auth: DN)
Chain Length:140
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60488 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L14
Chain IDs:SA (auth: BO), WC (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L15
Chain IDs:TA (auth: BP), XC (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L16
Chain IDs:UA (auth: BQ), YC (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60489 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L17
Chain IDs:VA (auth: BR), ZC (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L18
Chain IDs:WA (auth: BS), AD (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L19
Chain IDs:XA (auth: BT), BD (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60490 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L20
Chain IDs:YA (auth: BU), CD (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60491 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L21
Chain IDs:ZA (auth: BV), DD (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60492 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L22
Chain IDs:AB (auth: BW), ED (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP3 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L23
Chain IDs:BB (auth: BX), FD (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L24
Chain IDs:CB (auth: BY), GD (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L25
Chain IDs:DB (auth: BZ), HD (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
5MU	V	T	RIBOSYLTHYMINE-5'-MONOPHOSPHATE

Ligand Molecules

PAR

Primary Citation

Structure of the 70S ribosome complexed with mRNA and tRNA.

Selmer, M, Dunham, C.M, Murphy, F.V, Weixlbaumer, A, Petry, S, Kelley, A.C, Weir, J.R, Ramakrishnan, V.Show

Science 313 1935 1942 (2006)

PMID: 16959973 DOI: 10.1126/science.1131127

Abstact

The crystal structure of the bacterial 70S ribosome refined to 2.8 angstrom resolution reveals atomic details of its interactions with messenger RNA (mRNA) and transfer RNA (tRNA). A metal ion stabilizes a kink in the mRNA that demarcates the boundary between A and P sites, which is potentially important to prevent slippage of mRNA. Metal ions also stabilize the intersubunit interface. The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures