6Q95 image
Deposition Date 2018-12-17
Release Date 2019-02-27
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6Q95
Keywords:
RIBOSOME
Title:
Structure of tmRNA SmpB bound in A site of T. thermophilus 70S ribosome
Biological Source:
Source Organism:
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (Taxon ID: 300852)
Escherichia coli (Taxon ID: 562)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (Taxon ID: 262724)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6Q95 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:HA (auth: 1)
Chain Length:2915
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:16S RIBOSOMAL RNA
Chain IDs:A (auth: 2)
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:IA (auth: 3)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:transfer-messenger RNA (tmRNA)
Chain IDs:IB (auth: 4)
Chain Length:349
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SsrA-binding protein
Gene (Uniprot):smpB
Chain IDs:DB (auth: 5)
Chain Length:144
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q8RR57 Pfam ID:PF01668
Polymer Type:polypeptide(L)
Molecule:Nascent peptide MET-ALA
Chain IDs:EB (auth: 6)
Chain Length:2
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA-fMet
Chain IDs:V (auth: 7)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA-Phe
Chain IDs:W (auth: 8)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:X (auth: 9)
Chain Length:6
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:JA (auth: A)
Chain Length:229
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SLP7 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:KA (auth: B)
Chain Length:272
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:LA (auth: C)
Chain Length:45
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:MA (auth: D)
Chain Length:49
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:NA (auth: E)
Chain Length:64
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:OA (auth: F)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P0DOY8 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:PA (auth: G)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SLQ1 Pfam ID:PF01281
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L10 AND L11
Chain IDs:GB (auth: H), HB (auth: I)
Chain Length:207
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:QA (auth: J)
Chain Length:139
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:RA (auth: K)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:SA (auth: L)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:TA (auth: M)
Chain Length:136
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:UA (auth: N)
Chain Length:127
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:VA (auth: O)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:WA (auth: P)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:XA (auth: Q)
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:YA (auth: R)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:ZA (auth: S)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:AB (auth: T)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:BB (auth: U)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:CB (auth: V)
Chain Length:100
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHZ1 Pfam ID:PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:Y (auth: W)
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:Z (auth: X)
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:AA (auth: Y)
Chain Length:51
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:BA (auth: Z)
Chain Length:25
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:CA (auth: a)
Chain Length:229
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:DA (auth: b)
Chain Length:272
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:EA (auth: c)
Chain Length:45
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:FA (auth: d)
Chain Length:49
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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:GA (auth: e)
Chain Length:64
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SKU1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:FB (auth: f)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q5SHR2 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: g)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: h)
Chain Length:207
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: i)
Chain Length:140
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: j)
Chain Length:139
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: k)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: l)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P17291 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P0DOY9 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: o)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: p)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: q)
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: r)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80377 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:N (auth: s)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P0DOY6 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: t)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: u)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SJH3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: v)
Chain Length:100
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P0DOY7 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: w)
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: x)
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: y)
Chain Length:51
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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: z)
Chain Length:25
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SIH3 Pfam ID:PF17070
Ligand Molecules
MG
ZN
Primary Citation
How a circularized tmRNA moves through the ribosome.
Science 363 740 744 (2019)
PMID: 30765567 DOI: 10.1126/science.aav9370

Abstact

During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6Q97
6Q98
6Q9A