4V9I image
Deposition Date 2013-04-04
Release Date 2014-07-09
Last Version Date 2024-11-20
Entry Detail
PDB ID:
4V9I
Keywords:
RIBOSOME
Title:
Crystal structure of thermus thermophilus 70S in complex with tRNAs and mRNA containing a pseudouridine in a stop codon
Biological Source:
Source Organism:
Synthetic construct (Taxon ID: 32630)
Thermus thermophilus (Taxon ID: 300852)
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.30 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
4V9I validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA), GB (auth: CA)
Chain Length:1504
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), HB (auth: CB)
Chain Length:234
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC), IB (auth: CC)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD), JB (auth: CD)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE), KB (auth: CE)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF), LB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG), MB (auth: CG)
Chain Length:155
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S8
Chain IDs:H (auth: AH), NB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), OB (auth: CI)
Chain Length:127
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ), PB (auth: CJ)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK), QB (auth: CK)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL), RB (auth: CL)
Chain Length:124
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM), SB (auth: CM)
Chain Length:124
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S14
Chain IDs:N (auth: AN), TB (auth: CN)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO), UB (auth: CO)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP), VB (auth: CP)
Chain Length:83
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S17
Chain IDs:Q (auth: AQ), WB (auth: CQ)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), XB (auth: CR)
Chain Length:70
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS), YB (auth: CS)
Chain Length:78
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT), ZB (auth: CT)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein THX
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), AC (auth: CU)
Chain Length:24
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:P-SITE tRNA
Chain IDs:V (auth: AV), BC (auth: CV)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:E-SITE tRNA
Chain IDs:W (auth: AW), CC (auth: CW)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:Y (auth: AX)
Chain Length:7
Number of Molecules:1
Biological Source:Synthetic construct
Polymer Type:polyribonucleotide
Molecule:A-SITE tRNA
Chain IDs:X (auth: AY), DC (auth: CY)
Chain Length:75
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:WA (auth: B0), CD (auth: D0)
Chain Length:84
Number of Molecules:2
Biological Source:Thermus thermophilus
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:XA (auth: B1), DD (auth: D1)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60494 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:YA (auth: B2), ED (auth: D2)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:ZA (auth: B3), FD (auth: D3)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:AB (auth: B4), GD (auth: D4)
Chain Length:30
Number of Molecules:2
Biological Source:Thermus thermophilus
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:BB (auth: B5), HD (auth: D5)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80339 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:CB (auth: B6), ID (auth: D6)
Chain Length:44
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P35871 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:DB (auth: B7), JD (auth: D7)
Chain Length:48
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80340 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:EB (auth: B8), KD (auth: D8)
Chain Length:63
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SKU1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:FB (auth: B9), LD (auth: D9)
Chain Length:36
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHR2 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:Z (auth: BA), FC (auth: DA)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:AA (auth: BB), GC (auth: DB)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Chain IDs:BA (auth: BC)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:CA (auth: BD), IC (auth: DD)
Chain Length:271
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:DA (auth: BE), JC (auth: DE)
Chain Length:204
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN8 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:EA (auth: BF), KC (auth: DF)
Chain Length:207
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN9 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:FA (auth: BG), LC (auth: DG)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:GA (auth: BH), MC (auth: DH)
Chain Length:159
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:HA (auth: BI), NC (auth: DI)
Chain Length:145
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Chain IDs:IA (auth: BJ), OC (auth: DJ)
Chain Length:130
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:JA (auth: BN), PC (auth: DN)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60488 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:KA (auth: BO), QC (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP8 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:LA (auth: BP), RC (auth: DP)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:MA (auth: BQ), SC (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60489 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:NA (auth: BR), TC (auth: DR)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:OA (auth: BS), UC (auth: DS)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:PA (auth: BT), VC (auth: DT)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60490 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:QA (auth: BU), WC (auth: DU)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60491 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:RA (auth: BV), XC (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60492 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:SA (auth: BW), YC (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP3 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:TA (auth: BX), ZC (auth: DX)
Chain Length:92
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:UA (auth: BY), AD (auth: DY)
Chain Length:100
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:VA (auth: BZ), BD (auth: DZ)
Chain Length:176
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:EC (auth: CX)
Chain Length:4
Number of Molecules:1
Biological Source:Synthetic construct
Polymer Type:polypeptide(L)
Molecule:50S Ribosomal protein L1
Chain IDs:HC (auth: DC)
Chain Length:196
Number of Molecules:1
Biological Source:Thermus thermophilus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PSU Y U PSEUDOURIDINE-5'-MONOPHOSPHATE
Ligand Molecules
NA
Primary Citation
Unusual base pairing during the decoding of a stop codon by the ribosome.
Nature 500 107 110 (2013)
PMID: 23812587 DOI: 10.1038/nature12302

Abstact

During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine-purine base pairs. Here we determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA(Ser) bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which show an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4V9I
4K0L
4K0M
4K0P
4K0Q
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