ISDA

Deposition Date 2016-02-22

Release Date 2016-05-25

Last Version Date 2024-01-10

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 (Taxon ID: 562)
Thermus thermophilus HB8 (Taxon ID: 300852)
Escherichia coli K-12 (Taxon ID: 83333)

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

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
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), EB (auth: 1G)
Chain Length:1522
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

Polymer Type:polyribonucleotide
Molecule: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)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
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)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
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
Molecule: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)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
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
Molecule: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)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
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)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
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)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
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
Molecule: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)
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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
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)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
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
Molecule: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)
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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
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)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
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
Molecule:mRNA
Chain IDs:Y (auth: 4K), CC (auth: 4L)
Chain Length:30
Number of Molecules:2
Biological Source:Escherichia coli

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
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)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
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)
Molecule: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)
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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
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)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
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)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
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)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
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)
Molecule: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)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
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)
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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
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)
Molecule: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)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
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)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
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)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
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)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
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)
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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
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)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
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)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
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)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
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)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
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)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
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)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
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)
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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
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)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
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)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
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)
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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
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)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
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)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
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
5MU	V	U	modified residue
PSU	V	U	modified residue
T6A	V	A	modified residue

Ligand Molecules

PAR

SF4

SPE

Primary Citation

The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.

Rozov, A, Westhof, E, Yusupov, M, Yusupova, G.Show

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