ISDA: 9QF5

Deposition Date 2025-03-11

Release Date 2025-11-05

Last Version Date 2025-12-10

Entry Detail

PDB ID:

9QF5

Keywords:

RIBOSOME

Title:

Structure of P. furiosus 70S ribosome grown at 102deg

Biological Source:

Source Organism(s):

Pyrococcus furiosus (Taxon ID: 2261)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.84 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: A1)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps2
Chain IDs:B (auth: Aa)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0F0 Pfam ID:PF00318

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps3
Chain IDs:C (auth: Ab)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U004 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps3ae
Chain IDs:D (auth: Ac)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8TZE1 Pfam ID:PF01015

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps4
Chain IDs:E (auth: Ad)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:P61993 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps4e
Chain IDs:F (auth: Ae)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U011 Pfam ID:PF08071, PF01479, PF00900

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps5
Chain IDs:G (auth: Af)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U017 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps6e
Chain IDs:H (auth: Ag)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U3H8 Pfam ID:PF01092

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps7
Chain IDs:I (auth: Ah)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0M8 Pfam ID:PF00177

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps8
Chain IDs:J (auth: Ai)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U014 Pfam ID:PF00410

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps8e
Chain IDs:K (auth: Aj)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U1Y5 Pfam ID:PF01201

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps9
Chain IDs:L (auth: Ak)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0E7 Pfam ID:PF00380

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps10
Chain IDs:M (auth: Al)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:P61885 Pfam ID:PF00338

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps11
Chain IDs:N (auth: Am)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0E3 Pfam ID:PF00411

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps12
Chain IDs:O (auth: An)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:P61995 Pfam ID:PF00164

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps13
Chain IDs:P (auth: Ao)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0E2 Pfam ID:PF00416

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps14
Chain IDs:Q (auth: Ap)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U013 Pfam ID:PF00253

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps15
Chain IDs:R (auth: Aq)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8TZD9 Pfam ID:PF08069, PF00312

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps17
Chain IDs:S (auth: Ar)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U008 Pfam ID:PF00366

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps17e
Chain IDs:T (auth: As)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0U1 Pfam ID:PF00833

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps19
Chain IDs:U (auth: At)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U002 Pfam ID:PF00203

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps19e
Chain IDs:V (auth: Au)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0T4 Pfam ID:PF01090

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps24e
Chain IDs:W (auth: Av)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U442 Pfam ID:PF01282

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps27e
Chain IDs:X (auth: Aw)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U474 Pfam ID:PF01667

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps28e
Chain IDs:Y (auth: Ax)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U159 Pfam ID:PF01200

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Zn-ribbon RNA-binding protein
Gene (Uniprot):PFC_08760
Chain IDs:Z (auth: Ay)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:I6U991 Pfam ID:PF07754

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:AA (auth: B1)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:BA (auth: B2)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl2
Chain IDs:CA (auth: BA)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U001 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl3
Chain IDs:DA (auth: BB)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8TZZ8 Pfam ID:PF00297

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl4
Chain IDs:EA (auth: BC)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8TZZ9 Pfam ID:PF00573

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl5
Chain IDs:FA (auth: BD)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U012 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl6
Chain IDs:GA (auth: BE)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U015 Pfam ID:PF00347

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl7ae
Chain IDs:HA (auth: BF), IA (auth: BG)
Chain Length:0
Number of Molecules:2
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U160 Pfam ID:PF01248

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl10e
Chain IDs:JA (auth: BH)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q9UWP5 Pfam ID:PF00252

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl13
Chain IDs:KA (auth: BI)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0E6 Pfam ID:PF00572

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl14
Chain IDs:LA (auth: BJ)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U009 Pfam ID:PF00238

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl14e
Chain IDs:MA (auth: BK), NA (auth: BL)
Chain Length:0
Number of Molecules:2
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U2L5 Pfam ID:PF00467

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl15
Chain IDs:OA (auth: BM)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U018 Pfam ID:PF00828

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl15e
Chain IDs:PA (auth: BN)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U2F9 Pfam ID:PF00827

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl18
Chain IDs:QA (auth: BO)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q9HH80 Pfam ID:PF17144

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl18e
Chain IDs:RA (auth: BP)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0E5 Pfam ID:PF17135

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl19e
Chain IDs:SA (auth: BQ)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U016 Pfam ID:PF01280, PF25476

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl21e
Chain IDs:TA (auth: BR)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U217 Pfam ID:PF01157

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl22
Chain IDs:UA (auth: BS)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U003 Pfam ID:PF00237

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl23
Chain IDs:VA (auth: BT)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U000 Pfam ID:PF00276

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl24
Chain IDs:WA (auth: BU)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U010 Pfam ID:PF16906, PF00467

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl24e
Chain IDs:XA (auth: BV)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U158 Pfam ID:PF01246

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl29
Chain IDs:YA (auth: BW)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U005 Pfam ID:PF00831

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl30
Chain IDs:ZA (auth: BX)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q9HH78 Pfam ID:PF00327

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl30e
Chain IDs:AB (auth: BY)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0M6 Pfam ID:PF01248

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl31e
Chain IDs:BB (auth: BZ)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U3S7 Pfam ID:PF01198

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl32e
Chain IDs:CB (auth: Ba)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q9HH82 Pfam ID:PF01655

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl34e
Chain IDs:DB (auth: Bb)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U2L3 Pfam ID:PF01199

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl35ae
Chain IDs:EB (auth: Bc)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8TZV6 Pfam ID:PF01247

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl37e
Chain IDs:FB (auth: Bd)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0P5 Pfam ID:PF01907

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl37ae
Chain IDs:GB (auth: Be)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8TZI4 Pfam ID:PF01780

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl39e
Chain IDs:HB (auth: Bf)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U3S6 Pfam ID:PF00832

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl40e
Chain IDs:IB (auth: Bg)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U0V6

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpl41e
Chain IDs:JB (auth: Bh)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U232

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl44e
Chain IDs:KB (auth: Bi)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U475 Pfam ID:PF00935

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl18a
Chain IDs:LB (auth: Bj)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U3S9 Pfam ID:PF01775

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:C2H2-type domain-containing p
Gene (Uniprot):PF0829
Chain IDs:MB (auth: Bk)
Chain Length:0
Number of Molecules:1
Biological Source:Pyrococcus furiosus

UniProt ID:Q8U2K5 Pfam ID:PF00096

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
2MG	A	G	modified residue
4SU	A	U	modified residue
5MC	A	C	modified residue
5MU	A	U	modified residue
A1I59	A	C	modified residue
A2M	A	A	modified residue
G7M	A	G	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

Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome.

Garcia-Campos, M.A, Georgeson, J, Nir, R, Reichelt, R, Fluke, K.A, Matzov, D, Iyer, V, Burkhart, B.W, Lui, L, Kustanovich, A, Grunberger, F, Thalalla-Gamage, S, Howpay-Manage, S.A, Gerovac, M, Alexandre, N, Nobe, Y, Nowak, J.S, Perera, M, Apostle, A, Fang, S, Glatt, S, Jona, G, Ferreira-Cerca, S, Vogel, J, Taoka, M, Meier, J.L, Westhof, E, Santangelo, T.J, Grohmann, D, Shalev-Benami, M, Schwartz, S.Show

Cell 188 6825 ? (2025)

PMID: 41130207 DOI: 10.1016/j.cell.2025.09.014

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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