6GZX image
Deposition Date 2018-07-05
Release Date 2018-10-24
Last Version Date 2024-10-23
Entry Detail
PDB ID:
6GZX
Keywords:
RIBOSOME
Title:
T. thermophilus hibernating 100S ribosome (ice)
Biological Source:
Source Organism:
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (Taxon ID: 300852)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.57 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6GZX validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:CA (auth: A1), HB (auth: A2)
Chain Length:2912
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:FC (auth: A3), CD (auth: A4)
Chain Length:1506
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:DA (auth: B1), IB (auth: B2)
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 S2
Gene (Uniprot):rpsB
Chain IDs:KB (auth: B3), HC (auth: B4)
Chain Length:237
Number of Molecules:2
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), FA (auth: C2)
Chain Length:49
Number of Molecules:2
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:LB (auth: C3), IC (auth: C4)
Chain Length:206
Number of Molecules:2
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), GA (auth: D2)
Chain Length:205
Number of Molecules:2
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:MB (auth: D3), JC (auth: D4)
Chain Length:208
Number of Molecules:2
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:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:C (auth: E1), HA (auth: E2)
Chain Length:208
Number of Molecules:2
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:NB (auth: E3), KC (auth: E4)
Chain Length:151
Number of Molecules:2
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), IA (auth: F2)
Chain Length:181
Number of Molecules:2
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:OB (auth: F3), LC (auth: F4)
Chain Length:101
Number of Molecules:2
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), JA (auth: G2)
Chain Length:170
Number of Molecules:2
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:PB (auth: G3), MC (auth: G4)
Chain Length:155
Number of Molecules:2
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), KA (auth: H2)
Chain Length:50
Number of Molecules:2
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:QB (auth: H3), NC (auth: H4)
Chain Length:138
Number of Molecules:2
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), LA (auth: I2)
Chain Length:138
Number of Molecules:2
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:RB (auth: I3), OC (auth: I4)
Chain Length:127
Number of Molecules:2
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), MA (auth: J2)
Chain Length:122
Number of Molecules:2
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:SB (auth: J3), PC (auth: J4)
Chain Length:99
Number of Molecules:2
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), NA (auth: K2)
Chain Length:150
Number of Molecules:2
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:TB (auth: K3), QC (auth: K4)
Chain Length:118
Number of Molecules:2
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), OA (auth: L2)
Chain Length:141
Number of Molecules:2
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:UB (auth: L3), RC (auth: L4)
Chain Length:125
Number of Molecules:2
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), PA (auth: M2)
Chain Length:117
Number of Molecules:2
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:VB (auth: M3), SC (auth: M4)
Chain Length:117
Number of Molecules:2
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), QA (auth: N2)
Chain Length:111
Number of Molecules:2
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:WB (auth: N3), TC (auth: N4)
Chain Length:60
Number of Molecules:2
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), RA (auth: O2)
Chain Length:137
Number of Molecules:2
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:XB (auth: O3), UC (auth: O4)
Chain Length:88
Number of Molecules:2
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), SA (auth: P2)
Chain Length:117
Number of Molecules:2
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:YB (auth: P3), VC (auth: P4)
Chain Length:84
Number of Molecules:2
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), TA (auth: Q2)
Chain Length:101
Number of Molecules:2
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:ZB (auth: Q3), WC (auth: Q4)
Chain Length:100
Number of Molecules:2
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), UA (auth: R2)
Chain Length:113
Number of Molecules:2
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:AC (auth: R3), XC (auth: R4)
Chain Length:62
Number of Molecules:2
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), VA (auth: S2)
Chain Length:92
Number of Molecules:2
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:BC (auth: S3), YC (auth: S4)
Chain Length:78
Number of Molecules:2
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), WA (auth: T2)
Chain Length:102
Number of Molecules:2
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:CC (auth: T3), ZC (auth: T4)
Chain Length:99
Number of Molecules:2
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), XA (auth: U2)
Chain Length:179
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHZ1 Pfam ID:PF14693, PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:DC (auth: U3), AD (auth: U4)
Chain Length:25
Number of Molecules:2
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), YA (auth: V2)
Chain Length:77
Number of Molecules:2
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:GC (auth: V3), DD (auth: V4)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SIS0 Pfam ID:PF02482, PF16321
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:U (auth: W1), ZA (auth: W2)
Chain Length:97
Number of Molecules:2
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), AB (auth: X2)
Chain Length:69
Number of Molecules:2
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:Ribosome hibernation promoting factor
Gene (Uniprot):hpf
Chain IDs:EC (auth: X3), BD (auth: W4)
Chain Length:57
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SIS0 Pfam ID:PF02482, PF16321
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:W (auth: Y1), BB (auth: Y2)
Chain Length:59
Number of Molecules:2
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), CB (auth: Z2)
Chain Length:63
Number of Molecules:2
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), DB (auth: a2)
Chain Length:2912
Number of Molecules:2
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), EB (auth: b2)
Chain Length:122
Number of Molecules:2
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), FB (auth: c2)
Chain Length:49
Number of Molecules:2
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), GB (auth: d2)
Chain Length:205
Number of Molecules:2
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), JB (auth: e2)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHR2 Pfam ID:PF00444
Ligand Molecules
NA
Primary Citation
Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6GZQ