5IB7 image
Entry Detail
PDB ID:
5IB7
Keywords:
TRANSLATION
Title:
Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin
Biological Source:
Source Organism:
Escherichia coli, Thermus thermophilus HB8, Escherichia coli K-12
PDB Version:
Deposition Date:
2016-02-22
Release Date:
2016-05-25
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.99 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
5IB7 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:CA (auth: 11), FC (auth: 19)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:A (auth: 13), EB (auth: 1G)
Chain Length:1522
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:AA (auth: 16), EC (auth: 1J)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:B (auth: 1E), FB (auth: 12)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80371 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein Thx
Chain IDs:U (auth: 1F), YB (auth: 1B)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:Z (auth: 1H), DC (auth: 14)
Chain Length:2917
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:J (auth: 1I), NB (auth: 1A)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN7 Pfam ID:PF00338
Polymer Type:polyribonucleotide
Description:tRNALys
Chain IDs:V (auth: 1K)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:DA (auth: 21), GC (auth: 29)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN8 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:C (auth: 2E), GB (auth: 22)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:K (auth: 2I), OB (auth: 2A)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80376 Pfam ID:PF00411
Polymer Type:polyribonucleotide
Description:tRNAfMet
Chain IDs:W (auth: 2K), AC (auth: 2L)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:EA (auth: 31), HC (auth: 39)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN9 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:D (auth: 3E), HB (auth: 32)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:L (auth: 3I), PB (auth: 3A)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN3 Pfam ID:PF00164
Polymer Type:polyribonucleotide
Description:tRNALys
Chain IDs:X (auth: 3K), ZB (auth: 1L), BC (auth: 3L)
Chain Length:76
Number of Molecules:3
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:FA (auth: 41), IC (auth: 49)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:E (auth: 4E), IB (auth: 42)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:M (auth: 4I), QB (auth: 4A)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80377 Pfam ID:PF00416
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:Y (auth: 4K), CC (auth: 4L)
Chain Length:30
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:GA (auth: 51), JC (auth: 59)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:IA (auth: 58), LC (auth: 15)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60488 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:F (auth: 5E), JB (auth: 52)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP8 Pfam ID:PF01250
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14 type Z
Chain IDs:N (auth: 5I), RB (auth: 5A)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:HA (auth: 61), KC (auth: 69)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:JA (auth: 68), MC (auth: 25)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP8 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:G (auth: 6E), KB (auth: 62)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P17291 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:O (auth: 6I), SB (auth: 6A)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJ76 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L1
Chain IDs:BA (auth: 71)
Chain Length:229
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P27150 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:KA (auth: 78), NC (auth: 35)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:H (auth: 7E), LB (auth: 72)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:P (auth: 7I), TB (auth: 7A)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJH3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:LA (auth: 88), OC (auth: 45)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60489 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:I (auth: 8E), MB (auth: 82)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80374 Pfam ID:PF00380
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:Q (auth: 8I), UB (auth: 8A)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:MA (auth: 98), PC (auth: 55)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:R (auth: 9I), VB (auth: 9A)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:NA (auth: A8), QC (auth: 65)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:S (auth: AI), WB (auth: AA)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:OA (auth: B8), RC (auth: 75)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60490 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:T (auth: BI), XB (auth: BA)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80380 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:PA (auth: C8), SC (auth: 85)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60491 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:QA (auth: D8), TC (auth: 95)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60492 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:RA (auth: E8), UC (auth: A5)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP3 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:SA (auth: F8), VC (auth: B5)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:TA (auth: G8), WC (auth: C5)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:UA (auth: H8), XC (auth: D5)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:VA (auth: I8), YC (auth: E5)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60493 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:WA (auth: J8), ZC (auth: F5)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60494 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:XA (auth: K8), AD (auth: G5)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:YA (auth: L8), BD (auth: H5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:ZA (auth: M8)
Chain Length:71
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJE1 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:AB (auth: N8), CD (auth: J5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80339 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:BB (auth: O8)
Chain Length:54
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P35871 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:CB (auth: P8), DD (auth: L5)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80340 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:DB (auth: Q8), ED (auth: M5)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SKU1 Pfam ID:PF01632
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5MU V U modified residue
PSU V U modified residue
T6A V A modified residue
Ligand Molecules
MG
PAR
SF4
SPE
ZN
Primary Citation
The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.
Nucleic Acids Res. 44 6434 6441 (2016)
PMID: 27174928 DOI: 10.1093/nar/gkw431

Abstact

Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G•U base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical G•C pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
5IB7