6UCQ image
Deposition Date 2019-09-17
Release Date 2019-12-25
Last Version Date 2025-03-19
Entry Detail
PDB ID:
6UCQ
Keywords:
Title:
Crystal structure of the Thermus thermophilus 70S ribosome recycling complex
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.50 Å
R-Value Free:
0.29
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:U (auth: 10), YB (auth: 20)
Chain Length:85
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 L28
Gene (Uniprot):rpmB
Chain IDs:V (auth: 11), ZB (auth: 21)
Chain Length:98
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 L29
Gene (Uniprot):rpmC
Chain IDs:W (auth: 12), AC (auth: 22)
Chain Length:72
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 L30
Gene (Uniprot):rpmD
Chain IDs:X (auth: 13), BC (auth: 23)
Chain Length:60
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 L31
Gene (Uniprot):rpmE
Chain IDs:Y (auth: 14), CC (auth: 24)
Chain Length:71
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 L32
Gene (Uniprot):rpmF
Chain IDs:Z (auth: 15), DC (auth: 25)
Chain Length:60
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 L33
Gene (Uniprot):rpmG
Chain IDs:AA (auth: 16), EC (auth: 26)
Chain Length:54
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 L34
Gene (Uniprot):rpmH
Chain IDs:BA (auth: 17), FC (auth: 27)
Chain Length:49
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 L35
Gene (Uniprot):rpmI
Chain IDs:CA (auth: 18), GC (auth: 28)
Chain Length:65
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 L36
Gene (Uniprot):rpmJ
Chain IDs:DA (auth: 19), HC (auth: 29)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:A (auth: 1A), EB (auth: 2A)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:B (auth: 1B), FB (auth: 2B)
Chain Length:121
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: 1D), GB (auth: 2D)
Chain Length:276
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 L3
Gene (Uniprot):rplC
Chain IDs:D (auth: 1E), HB (auth: 2E)
Chain Length:206
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 L4
Gene (Uniprot):rplD
Chain IDs:E (auth: 1F), IB (auth: 2F)
Chain Length:101
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 L5
Gene (Uniprot):rplE
Chain IDs:F (auth: 1G), JB (auth: 2G)
Chain Length:156
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 L6
Gene (Uniprot):rplF
Chain IDs:G (auth: 1H), KB (auth: 2H)
Chain Length:138
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:H (auth: 1N), LB (auth: 2N)
Chain Length:61
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 L14
Gene (Uniprot):rplN
Chain IDs:I (auth: 1O), MB (auth: 2O)
Chain Length:122
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 L15
Gene (Uniprot):rplO
Chain IDs:J (auth: 1P), NB (auth: 2P)
Chain Length:88
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 L16
Gene (Uniprot):rplP
Chain IDs:K (auth: 1Q), OB (auth: 2Q)
Chain Length:105
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 L17
Gene (Uniprot):rplQ
Chain IDs:L (auth: 1R), PB (auth: 2R)
Chain Length:88
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 L18
Gene (Uniprot):rplR
Chain IDs:M (auth: 1S), QB (auth: 2S)
Chain Length:93
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 L19
Gene (Uniprot):rplS
Chain IDs:N (auth: 1T), RB (auth: 2T)
Chain Length:146
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 L20
Gene (Uniprot):rplT
Chain IDs:O (auth: 1U), SB (auth: 2U)
Chain Length:27
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 L21
Gene (Uniprot):rplU
Chain IDs:P (auth: 1V), TB (auth: 2V)
Chain Length:758
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 L22
Gene (Uniprot):rplV
Chain IDs:Q (auth: 1W), UB (auth: 2W)
Chain Length:113
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 L23
Gene (Uniprot):rplW
Chain IDs:R (auth: 1X), VB (auth: 2X)
Chain Length:76
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 L24
Gene (Uniprot):rplX
Chain IDs:S (auth: 1Y), WB (auth: 2Y)
Chain Length:110
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 L25
Gene (Uniprot):rplY
Chain IDs:T (auth: 1Z), XB (auth: 2Z)
Chain Length:21
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:EA (auth: 1a), IC (auth: 2a)
Chain Length:2915
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
Gene (Uniprot):rpsB
Chain IDs:FA (auth: 1b), JC (auth: 2b)
Chain Length:121
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:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:GA (auth: 1c), KC (auth: 2c)
Chain Length:239
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:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:HA (auth: 1d), LC (auth: 2d)
Chain Length:276
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:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:IA (auth: 1e), MC (auth: 2e)
Chain Length:206
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:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:JA (auth: 1f), NC (auth: 2f)
Chain Length:101
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:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:KA (auth: 1g), OC (auth: 2g)
Chain Length:156
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:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:LA (auth: 1h), PC (auth: 2h)
Chain Length:138
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:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:MA (auth: 1i), QC (auth: 2i)
Chain Length:128
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:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:NA (auth: 1j), RC (auth: 2j)
Chain Length:105
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:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:OA (auth: 1k), SC (auth: 2k)
Chain Length:129
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:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:PA (auth: 1l), TC (auth: 2l)
Chain Length:132
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:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:QA (auth: 1m), UC (auth: 2m)
Chain Length:126
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:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:RA (auth: 1n), VC (auth: 2n)
Chain Length:61
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:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:SA (auth: 1o), WC (auth: 2o)
Chain Length:122
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:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:TA (auth: 1p), XC (auth: 2p)
Chain Length:88
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:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:UA (auth: 1q), YC (auth: 2q)
Chain Length:105
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:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: 1r), ZC (auth: 2r)
Chain Length:88
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:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:WA (auth: 1s), AD (auth: 2s)
Chain Length:93
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:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: 1t), BD (auth: 2t)
Chain Length:146
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:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:YA (auth: 1u), CD (auth: 2u)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9,Elongation factor G
Gene (Uniprot):fusA, rplI
Chain IDs:ZA (auth: 1v), DD (auth: 2v)
Chain Length:758
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:Ribosome-recycling factor
Gene (Uniprot):frr
Chain IDs:AB (auth: 1w), ED (auth: 2w)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:P-site and E-site tRNAs
Chain IDs:BB (auth: 1x), CB (auth: 1y), FD (auth: 2x), GD (auth: 2y)
Chain Length:76
Number of Molecules:4
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:DB (auth: 1z), HD (auth: 2z)
Chain Length:21
Number of Molecules:2
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD PA ASP modified residue
Primary Citation
Structural basis for ribosome recycling by RRF and tRNA.
Nat.Struct.Mol.Biol. 27 25 32 (2020)
PMID: 31873307 DOI: 10.1038/s41594-019-0350-7

Abstact

The bacterial ribosome is recycled into subunits by two conserved proteins, elongation factor G (EF-G) and the ribosome recycling factor (RRF). The molecular basis for ribosome recycling by RRF and EF-G remains unclear. Here, we report the crystal structure of a posttermination Thermus thermophilus 70S ribosome complexed with EF-G, RRF and two transfer RNAs at a resolution of 3.5 Å. The deacylated tRNA in the peptidyl (P) site moves into a previously unsuspected state of binding (peptidyl/recycling, p/R) that is analogous to that seen during initiation. The terminal end of the p/R-tRNA forms nonfavorable contacts with the 50S subunit while RRF wedges next to central inter-subunit bridges, illuminating the active roles of tRNA and RRF in dissociation of ribosomal subunits. The structure uncovers a missing snapshot of tRNA as it transits between the P and exit (E) sites, providing insights into the mechanisms of ribosome recycling and tRNA translocation.

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