ISDA: 6GZQ

Deposition Date 2018-07-04

Release Date 2018-10-24

Last Version Date 2024-11-13

Entry Detail

PDB ID:

6GZQ

Keywords:

RIBOSOME

Title:

T. thermophilus hibernating 70S ribosome

Biological Source:

Source Organism(s):

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (Taxon ID: 300852)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.28 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:CA (auth: A1)
Chain Length:2912
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:AB (auth: A2)
Chain Length:1506
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:DA (auth: B1)
Chain Length:122
Number of Molecules:1
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: B2)
Chain Length:237
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:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:A (auth: C1)
Chain Length:49
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60405 Pfam ID:PF03947, PF00181

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:GA (auth: C2)
Chain Length:206
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:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:B (auth: D1)
Chain Length:205
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:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:HA (auth: D2)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:C (auth: E1)
Chain Length:208
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:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:IA (auth: E2)
Chain Length:151
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:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:D (auth: F1)
Chain Length:181
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:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:JA (auth: F2)
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:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:E (auth: G1)
Chain Length:170
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:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:KA (auth: G2)
Chain Length:155
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:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:F (auth: H1)
Chain Length:50
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SLQ1 Pfam ID:PF01281

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:LA (auth: H2)
Chain Length:138
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:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:G (auth: I1)
Chain Length:138
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:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:MA (auth: I2)
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:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:H (auth: J1)
Chain Length:122
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:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:NA (auth: J2)
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:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:I (auth: K1)
Chain Length:150
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:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:OA (auth: K2)
Chain Length:118
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:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:J (auth: L1)
Chain Length:141
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:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:PA (auth: L2)
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:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:K (auth: M1)
Chain Length:117
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:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:QA (auth: M2)
Chain Length:117
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:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:L (auth: N1)
Chain Length:111
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:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:RA (auth: N2)
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:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:M (auth: O1)
Chain Length:137
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:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:SA (auth: O2)
Chain Length:88
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:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:N (auth: P1)
Chain Length:117
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:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:TA (auth: P2)
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:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:O (auth: Q1)
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:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:UA (auth: Q2)
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:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:P (auth: R1)
Chain Length:113
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:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: R2)
Chain Length:62
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:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:Q (auth: S1)
Chain Length:92
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:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:WA (auth: S2)
Chain Length:78
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:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:R (auth: T1)
Chain Length:102
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:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: T2)
Chain Length:99
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:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:S (auth: U1)
Chain Length:179
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:YA (auth: U2)
Chain Length:25
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SIH3 Pfam ID:PF17070

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:T (auth: V1)
Chain Length:77
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:Ribosome hibernation promoting factor
Gene (Uniprot):hpf
Chain IDs:ZA (auth: V2)
Chain Length:121
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SIS0 Pfam ID:PF02482

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:U (auth: W1)
Chain Length:97
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:V (auth: X1)
Chain Length:69
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:W (auth: Y1)
Chain Length:59
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:X (auth: Z1)
Chain Length:63
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:Y (auth: a1)
Chain Length:2912
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:Z (auth: b1)
Chain Length:122
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:AA (auth: c1)
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:BA (auth: d1)
Chain Length:205
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
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: e1)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHR2 Pfam ID:PF00444

Ligand Molecules

Primary Citation

Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.

Flygaard, R.K, Boegholm, N, Yusupov, M, Jenner, L.B.Show

Nat Commun 9 4179 4179 (2018)

PMID: 30301898 DOI: 10.1038/s41467-018-06724-x

Abstact

In response to cellular stresses bacteria conserve energy by dimerization of ribosomes into inactive hibernating 100S ribosome particles. Ribosome dimerization in Thermus thermophilus is facilitated by hibernation-promoting factor (TtHPF). In this study we demonstrate high sensitivity of Tt100S formation to the levels of TtHPF and show that a 1:1 ratio leads to optimal dimerization. We report structures of the T. thermophilus 100S ribosome determined by cryo-electron microscopy to average resolutions of 4.13 Å and 4.57 Å. In addition, we present a 3.28 Å high-resolution cryo-EM reconstruction of a 70S ribosome from a hibernating ribosome dimer and reveal a role for the linker region connecting the TtHPF N- and C-terminal domains in translation inhibition by preventing Shine-Dalgarno duplex formation. Our work demonstrates that species-specific differences in the dimerization interface govern the overall conformation of the 100S ribosome particle and that for Thermus thermophilus no ribosome-ribosome interactions are involved in the interface.

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Primary Citation of related structures

Abstact

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