9QF6 image
Deposition Date 2025-03-11
Release Date 2025-11-05
Last Version Date 2025-12-10
Entry Detail
PDB ID:
9QF6
Keywords:
Title:
Structure of P. furiosus 70S ribosome in RsmB deleted strain
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.67 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: A1)
Chain Length:1497
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rps2
Chain IDs:B (auth: Aa)
Chain Length:202
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rps3
Chain IDs:C (auth: Ab)
Chain Length:210
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS1
Gene (Uniprot):rps3ae
Chain IDs:D (auth: Ac)
Chain Length:198
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rps4
Chain IDs:E (auth: Ad)
Chain Length:180
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS4
Gene (Uniprot):rps4e
Chain IDs:F (auth: Ae)
Chain Length:243
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rps5
Chain IDs:G (auth: Af)
Chain Length:236
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS6
Gene (Uniprot):rps6e
Chain IDs:H (auth: Ag)
Chain Length:125
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rps7
Chain IDs:I (auth: Ah)
Chain Length:215
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rps8
Chain IDs:J (auth: Ai)
Chain Length:130
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS8
Gene (Uniprot):rps8e
Chain IDs:K (auth: Aj)
Chain Length:127
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rps9
Chain IDs:L (auth: Ak)
Chain Length:135
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rps10
Chain IDs:M (auth: Al)
Chain Length:102
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rps11
Chain IDs:N (auth: Am)
Chain Length:137
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rps12
Chain IDs:O (auth: An)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rps13
Chain IDs:P (auth: Ao)
Chain Length:148
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rps14
Chain IDs:Q (auth: Ap)
Chain Length:56
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rps15
Chain IDs:R (auth: Aq)
Chain Length:158
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rps17
Chain IDs:S (auth: Ar)
Chain Length:113
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS17
Gene (Uniprot):rps17e
Chain IDs:T (auth: As)
Chain Length:67
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rps19
Chain IDs:U (auth: At)
Chain Length:132
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS19
Gene (Uniprot):rps19e
Chain IDs:V (auth: Au)
Chain Length:150
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS24
Gene (Uniprot):rps24e
Chain IDs:W (auth: Av), NB (auth: Bl)
Chain Length:99
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS27
Gene (Uniprot):rps27e
Chain IDs:X (auth: Aw)
Chain Length:63
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS28
Gene (Uniprot):rps28e
Chain IDs:Y (auth: Ax)
Chain Length:71
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Zn-ribbon RNA-binding protein
Gene (Uniprot):PFC_08760
Chain IDs:Z (auth: Az)
Chain Length:60
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:AA (auth: B1)
Chain Length:3051
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:BA (auth: B2)
Chain Length:125
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rpl2
Chain IDs:CA (auth: BA)
Chain Length:130
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):rpl3
Chain IDs:DA (auth: BB)
Chain Length:365
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rpl4
Chain IDs:EA (auth: BC)
Chain Length:87
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rpl5
Chain IDs:FA (auth: BD)
Chain Length:186
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rpl6
Chain IDs:GA (auth: BE)
Chain Length:184
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL8
Gene (Uniprot):rpl7ae
Chain IDs:HA (auth: BF), IA (auth: BG)
Chain Length:51
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rpl10e
Chain IDs:JA (auth: BH)
Chain Length:181
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rpl13
Chain IDs:KA (auth: BI)
Chain Length:94
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rpl14
Chain IDs:LA (auth: BJ)
Chain Length:77
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL14
Gene (Uniprot):rpl14e
Chain IDs:MA (auth: BK), NA (auth: BL)
Chain Length:64
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rpl15
Chain IDs:OA (auth: BM)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL15
Gene (Uniprot):rpl15e
Chain IDs:PA (auth: BN)
Chain Length:194
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rpl18
Chain IDs:QA (auth: BO)
Chain Length:203
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL18
Gene (Uniprot):rpl18e
Chain IDs:RA (auth: BP)
Chain Length:120
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL19
Gene (Uniprot):rpl19e
Chain IDs:SA (auth: BQ)
Chain Length:150
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL21
Gene (Uniprot):rpl21e
Chain IDs:TA (auth: BR)
Chain Length:97
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rpl22
Chain IDs:UA (auth: BS)
Chain Length:155
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rpl23
Chain IDs:VA (auth: BT)
Chain Length:86
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rpl24
Chain IDs:WA (auth: BU)
Chain Length:121
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL24
Gene (Uniprot):rpl24e
Chain IDs:XA (auth: BV)
Chain Length:66
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpl29
Chain IDs:YA (auth: BW)
Chain Length:72
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpl30
Chain IDs:ZA (auth: BX)
Chain Length:155
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL30
Gene (Uniprot):rpl30e
Chain IDs:AB (auth: BY)
Chain Length:99
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL31
Gene (Uniprot):rpl31e
Chain IDs:BB (auth: BZ)
Chain Length:95
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL32
Gene (Uniprot):rpl32e
Chain IDs:CB (auth: Ba)
Chain Length:130
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL34
Gene (Uniprot):rpl34e
Chain IDs:DB (auth: Bb)
Chain Length:365
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL33
Gene (Uniprot):rpl35ae
Chain IDs:EB (auth: Bc)
Chain Length:87
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL37
Gene (Uniprot):rpl37e
Chain IDs:FB (auth: Bd)
Chain Length:186
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL43
Gene (Uniprot):rpl37ae
Chain IDs:GB (auth: Be)
Chain Length:184
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL39
Gene (Uniprot):rpl39e
Chain IDs:HB (auth: Bf)
Chain Length:51
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL40
Gene (Uniprot):rpl40e
Chain IDs:IB (auth: Bg)
Chain Length:123
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS32
Gene (Uniprot):rpl41e
Chain IDs:JB (auth: Bh)
Chain Length:181
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL42
Gene (Uniprot):rpl44e
Chain IDs:KB (auth: Bi)
Chain Length:94
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL20
Gene (Uniprot):rpl18a
Chain IDs:LB (auth: Bj)
Chain Length:77
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:C2H2-type domain-containing protein
Gene (Uniprot):PF0829
Chain IDs:MB (auth: Bk)
Chain Length:64
Number of Molecules:1
Biological Source:Pyrococcus furiosus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4SU A U modified residue
5MC A C modified residue
5MU A U modified residue
A2M A A modified residue
LHH A C modified residue
MA6 A A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
Ligand Molecules
Primary Citation

Abstact

Ribosomal RNA (rRNA) constitutes the core of ribosomes and is extensively chemically modified. Technical challenges have precluded systematically dissecting rRNA modifications and their dynamics. We develop Pan-Mod-seq, permitting inference of 16 distinct modifications across dozens of samples in parallel. We applied Pan-Mod-seq to RNA from 14 species spanning all domains of life, cultured under highly diverse conditions. While dynamic modifications are rare in mesophiles, in extreme hyperthermophiles, ∼50% of modifications are dynamic. We dissect the biogenesis and function of a conserved module of tandem m5C-ac4C modifications, co-induced at high temperatures, via enzymes intrinsically regulated by temperature and required for growth at higher temperatures. Cryo-electron microscopy (cryo-EM) structures of ribosomes from wild-type (WT) and enzyme-deficient archaea reveal recurrent molecular interactions through which they confer structural stability, and biophysical studies demonstrate their synergistic thermostabilizing role. Our findings systematically dissect rRNA modification plasticity and pave the way for surveying the rRNA epitranscriptome in health and disease.

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Protein

Chemical

Disease

Primary Citation of related structures
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