9ZNF image
Deposition Date 2025-12-12
Release Date 2026-01-28
Last Version Date 2026-07-01
Entry Detail
PDB ID:
9ZNF
Keywords:
Title:
Cryo-EM structure of the Methanosarcina acetivorans 70S ribosome in complex with SriA and SriB
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.03 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A (auth: 1)
Chain Length:2904
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B (auth: 2)
Chain Length:133
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:C (auth: 3)
Chain Length:1478
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:CBS domain-containing protein
Gene (Uniprot):HA338_08675
Chain IDs:E (auth: 4)
Chain Length:270
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:CBS domain-containing protein
Gene (Uniprot):HA338_08680
Chain IDs:D (auth: 5)
Chain Length:339
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:F (auth: 8)
Chain Length:75
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl2
Chain IDs:G (auth: AA)
Chain Length:238
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl3
Chain IDs:H (auth: AB)
Chain Length:337
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl4
Chain IDs:I (auth: AC)
Chain Length:253
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl5
Chain IDs:J (auth: AD)
Chain Length:165
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl6
Chain IDs:K (auth: AE)
Chain Length:176
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl7ae
Chain IDs:L (auth: AF)
Chain Length:120
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl13
Chain IDs:M (auth: AG)
Chain Length:143
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl14
Chain IDs:N (auth: AH)
Chain Length:132
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl15
Chain IDs:O (auth: AI)
Chain Length:140
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl15e
Chain IDs:P (auth: AJ)
Chain Length:196
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl10e
Chain IDs:Q (auth: AK)
Chain Length:173
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl18
Chain IDs:R (auth: AL)
Chain Length:174
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl18e
Chain IDs:S (auth: AM)
Chain Length:126
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl19e
Chain IDs:T (auth: AN)
Chain Length:151
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl18a
Chain IDs:U (auth: AO)
Chain Length:61
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl21e
Chain IDs:V (auth: AP)
Chain Length:97
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl22
Chain IDs:W (auth: AQ)
Chain Length:151
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl23
Chain IDs:X (auth: AR)
Chain Length:82
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl24
Chain IDs:Y (auth: AS)
Chain Length:119
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl24e
Chain IDs:Z (auth: AT)
Chain Length:62
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl29
Chain IDs:AA (auth: AU)
Chain Length:67
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl30
Chain IDs:BA (auth: AV)
Chain Length:153
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl30e
Chain IDs:CA (auth: AW)
Chain Length:99
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl31e
Chain IDs:DA (auth: AX)
Chain Length:89
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl32e
Chain IDs:EA (auth: AY)
Chain Length:129
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl37e
Chain IDs:FA (auth: AZ)
Chain Length:56
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl39e
Chain IDs:GA (auth: Aa)
Chain Length:51
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl40e
Chain IDs:HA (auth: Ab)
Chain Length:49
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl44e
Chain IDs:IA (auth: Ac)
Chain Length:92
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpl37ae
Chain IDs:JA (auth: Ad)
Chain Length:94
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps3ae
Chain IDs:KA (auth: BA)
Chain Length:203
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps2
Chain IDs:LA (auth: BB)
Chain Length:225
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps3
Chain IDs:MA (auth: BC)
Chain Length:318
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps4
Chain IDs:NA (auth: BD)
Chain Length:218
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps4e
Chain IDs:OA (auth: BE)
Chain Length:235
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps5
Chain IDs:PA (auth: BF)
Chain Length:209
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps6e
Chain IDs:QA (auth: BG)
Chain Length:136
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps7
Chain IDs:RA (auth: BH)
Chain Length:189
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps8
Chain IDs:SA (auth: BI)
Chain Length:130
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps9
Chain IDs:TA (auth: BJ)
Chain Length:134
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps8e
Chain IDs:UA (auth: BK)
Chain Length:125
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps10
Chain IDs:VA (auth: BL)
Chain Length:102
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps11
Chain IDs:WA (auth: BM)
Chain Length:126
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps12
Chain IDs:XA (auth: BN)
Chain Length:142
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps13
Chain IDs:YA (auth: BO)
Chain Length:162
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps14
Chain IDs:ZA (auth: BP)
Chain Length:50
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps15
Chain IDs:AB (auth: BQ)
Chain Length:152
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps17-1
Chain IDs:BB (auth: BR)
Chain Length:109
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps17e
Chain IDs:CB (auth: BS)
Chain Length:64
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps19
Chain IDs:DB (auth: BT)
Chain Length:136
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps19e
Chain IDs:EB (auth: BU)
Chain Length:149
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Putative zinc finger domain-c
Gene (Uniprot):HA338_09005
Chain IDs:FB (auth: BV)
Chain Length:56
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps24e
Chain IDs:GB (auth: BW)
Chain Length:101
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps27e
Chain IDs:HB (auth: BX)
Chain Length:62
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rps28e
Chain IDs:IB (auth: BY)
Chain Length:76
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Polymer Type:polypeptide(L)
Molecule:DUF5350 family protein
Gene (Uniprot):HA338_12110
Chain IDs:JB (auth: BZ)
Chain Length:57
Number of Molecules:1
Biological Source:Methanosarcina acetivorans
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5MC A C modified residue
5MU C U modified residue
6MZ C A modified residue
MA6 C A modified residue
OMG A G modified residue
OMU A U modified residue
Primary Citation
A family of archaeal hibernation factors that bind in tandem and protect ribosomes in dormant cells.
Biorxiv ? ? ? (2026)
PMID: 41867869 DOI: 10.64898/2026.01.19.700200

Abstact

Under nutrient limitation or stress, ribosome hibernation factors inactivate and protect ribosomes. Although ribosome hibernation plays an important role in microbes, we lack a complete understanding of this process in archaea. Here, we identify a family of hibernation factors, which we designate as single ribosomal subunit inhibitors (SriA-SriD), from the methanogenic archaeon Methanosarcina acetivorans. All four sri genes are encoded in an operon and each Sri protein inhibits protein synthesis in vitro. Deletion of sri genes in M. acetivorans impaired growth recovery after prolonged stationary phase and also led to depletion of the small ribosomal subunit. Cryo-EM structures show that Sri proteins bind to the ribosome in tandem and form conserved protein-protein interfaces. Sri is broadly distributed across archaeal phyla and sri genes frequently co-occur. Together, these findings establish Sri proteins as a distinct group of hibernation factors that protect ribosomes during dormancy and expand our understanding of ribosome hibernation in archaea.

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Chemical

Disease

Primary Citation of related structures
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