5E81 image
Deposition Date 2015-10-13
Release Date 2016-01-27
Last Version Date 2024-01-10
Entry Detail
PDB ID:
5E81
Keywords:
RIBOSOME
Title:
Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Thermus thermophilus HB8 (Taxon ID: 300852)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.95 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
5E81 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Molecule:16S ribosomal RNA
Chain IDs:A (auth: 13), DB (auth: 1G)
Chain Length:1519
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:AA (auth: 16), DC (auth: 1J)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:B (auth: 1E), EB (auth: 12)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Chain IDs:U (auth: 1F), XB (auth: 1B)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:Z (auth: 1H), CC (auth: 14)
Chain Length:2917
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:J (auth: 1I), MB (auth: 1A)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN7 Pfam ID:PF00338
Polymer Type:polyribonucleotide
Molecule:tRNA-Lys
Chain IDs:V (auth: 1K), YB (auth: 1L)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:C (auth: 2E), FB (auth: 22)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:K (auth: 2I), NB (auth: 2A)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80376 Pfam ID:PF00411
Polymer Type:polyribonucleotide
Molecule:tRNA-fMet
Chain IDs:W (auth: 2K), ZB (auth: 2L)
Chain Length:77
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:D (auth: 3E), GB (auth: 32)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:L (auth: 3I), OB (auth: 3A)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN3 Pfam ID:PF00164
Polymer Type:polyribonucleotide
Molecule:tRNA-Lys
Chain IDs:X (auth: 3K), AC (auth: 3L)
Chain Length:76
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:E (auth: 4E), HB (auth: 42)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:M (auth: 4I), PB (auth: 4A)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80377 Pfam ID:PF00416
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:Y (auth: 4K), BC (auth: 4L)
Chain Length:27
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:GA (auth: 51), JC (auth: 59)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY8 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:F (auth: 5E), IB (auth: 52)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:N (auth: 5I), QB (auth: 5A)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY6 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:G (auth: 6E), JB (auth: 62)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P17291 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:O (auth: 6I), RB (auth: 6A)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Chain IDs:BA (auth: 71), EC (auth: 79)
Chain Length:229
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP7 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:H (auth: 7E), KB (auth: 72)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY9 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:P (auth: 7I), SB (auth: 7A)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJH3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: 8E), LB (auth: 82)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:Q (auth: 8I), TB (auth: 8A)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY7 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:R (auth: 9I), UB (auth: 9A)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:S (auth: AI), VB (auth: AA)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: BI), WB (auth: BA)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80380 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:BB (auth: P8), DD (auth: L5)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80340 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:CB (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
SF4
ZN
Primary Citation
Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
Nat Commun 7 10457 10457 (2016)
PMID: 26791911 DOI: 10.1038/ncomms10457

Abstact

Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
5E81