9E7F image
Deposition Date 2024-11-01
Release Date 2024-11-20
Last Version Date 2025-08-13
Entry Detail
PDB ID:
9E7F
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri
Biological Source:
Source Organism:
Pyrobaculum calidifontis JCM 11548 (Taxon ID: 410359)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.53 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9E7F validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:C (auth: 1)
Chain Length:3024
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:A (auth: 2)
Chain Length:129
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Putative signal-transduction protein with CBS domains
Gene (Uniprot):Pcal_1808
Chain IDs:B (auth: 3)
Chain Length:655
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX58 Pfam ID:PF00571
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:D (auth: 4)
Chain Length:1498
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rpl2
Chain IDs:E (auth: AA)
Chain Length:244
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS41 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):rpl3
Chain IDs:F (auth: AB)
Chain Length:338
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWI4 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rpl4
Chain IDs:G (auth: AC)
Chain Length:84
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWI5 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rpl5
Chain IDs:H (auth: AD)
Chain Length:178
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXP8 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rpl6
Chain IDs:I (auth: AE)
Chain Length:67
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWV5 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL8
Gene (Uniprot):rpl7ae
Chain IDs:J (auth: AF)
Chain Length:149
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTA9 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rpl13
Chain IDs:K (auth: AG)
Chain Length:53
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ7 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL13
Gene (Uniprot):rpl13e
Chain IDs:L (auth: AH)
Chain Length:157
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTP8 Pfam ID:PF01294
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rpl14
Chain IDs:M (auth: AI)
Chain Length:144
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX34 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL14
Gene (Uniprot):rpl14e
Chain IDs:N (auth: AJ), O (auth: AK)
Chain Length:103
Number of Molecules:2
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS76
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rpl15
Chain IDs:P (auth: AL)
Chain Length:156
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUZ1 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15e
Gene (Uniprot):Pcal_1666
Chain IDs:Q (auth: AM)
Chain Length:189
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWR6 Pfam ID:PF00827
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rpl10e
Chain IDs:R (auth: AN)
Chain Length:178
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXP3 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rpl18
Chain IDs:S (auth: AO)
Chain Length:205
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ3 Pfam ID:PF17144
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL18
Gene (Uniprot):rpl18e
Chain IDs:T (auth: AP)
Chain Length:122
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ6 Pfam ID:PF17135
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL19
Gene (Uniprot):rpl19e
Chain IDs:U (auth: AQ)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ4 Pfam ID:PF01280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL20
Gene (Uniprot):rpl18a
Chain IDs:V (auth: AR)
Chain Length:78
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX77 Pfam ID:PF01775
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL21
Gene (Uniprot):rpl21e
Chain IDs:W (auth: AS)
Chain Length:99
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWX9 Pfam ID:PF01157
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rpl22
Chain IDs:X (auth: AT)
Chain Length:184
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTL6 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rpl23
Chain IDs:Y (auth: AU)
Chain Length:81
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWI6 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rpl24
Chain IDs:Z (auth: AV)
Chain Length:128
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWZ8 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL24
Gene (Uniprot):rpl24e
Chain IDs:AA (auth: AW)
Chain Length:62
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTA8 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpl29
Chain IDs:BA (auth: AX)
Chain Length:79
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTL2 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpl30
Chain IDs:CA (auth: AY)
Chain Length:179
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MU87 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL30
Gene (Uniprot):rpl30e
Chain IDs:DA (auth: AZ)
Chain Length:101
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ2 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL31
Gene (Uniprot):rpl31e
Chain IDs:EA (auth: Aa)
Chain Length:244
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX75 Pfam ID:PF01198
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL32
Gene (Uniprot):rpl32e
Chain IDs:FA (auth: Ab)
Chain Length:338
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ5 Pfam ID:PF01655
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL34
Gene (Uniprot):rpl34e
Chain IDs:GA (auth: Ac)
Chain Length:84
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MV68 Pfam ID:PF01199
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL37
Gene (Uniprot):rpl37e
Chain IDs:HA (auth: Ad)
Chain Length:178
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MY38 Pfam ID:PF01907
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:LSU ribosomal protein L38E
Gene (Uniprot):Pcal_0622
Chain IDs:IA (auth: Ae)
Chain Length:67
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTT1 Pfam ID:PF01781
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL39
Gene (Uniprot):rpl39e
Chain IDs:JA (auth: Af)
Chain Length:149
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUU4 Pfam ID:PF00832
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL40
Gene (Uniprot):rpl40e
Chain IDs:KA (auth: Ag)
Chain Length:53
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX99 Pfam ID:PF01020
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL42
Chain IDs:LA (auth: Ah)
Chain Length:157
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUV1 Pfam ID:PF00935
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL43
Gene (Uniprot):rpl37ae
Chain IDs:MA (auth: Ai)
Chain Length:144
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUM7 Pfam ID:PF01780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DJ-1/PfpI domain-containing protein
Gene (Uniprot):Pcal_0567
Chain IDs:NA (auth: Aj)
Chain Length:103
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTM7 Pfam ID:PF01965
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:PaREP1 domain containing protein
Gene (Uniprot):Pcal_1690
Chain IDs:OA (auth: Ak)
Chain Length:93
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWU0
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS1
Gene (Uniprot):rps3ae
Chain IDs:PA (auth: BA)
Chain Length:54
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MVE0 Pfam ID:PF01015
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rps2
Chain IDs:QA (auth: BB)
Chain Length:208
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS50 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rps3
Chain IDs:RA (auth: BC)
Chain Length:216
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTL3 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rps4
Chain IDs:SA (auth: BD)
Chain Length:159
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUS9 Pfam ID:PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS4
Gene (Uniprot):rps4e
Chain IDs:TA (auth: BE)
Chain Length:237
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWZ7 Pfam ID:PF01479, PF08071, PF00900
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rps5
Chain IDs:UA (auth: BF)
Chain Length:202
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MU88 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS6
Gene (Uniprot):rps6e
Chain IDs:VA (auth: BG)
Chain Length:151
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUD0 Pfam ID:PF01092
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rps7
Chain IDs:WA (auth: BH)
Chain Length:223
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS29 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rps8
Chain IDs:XA (auth: BI)
Chain Length:130
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ6 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS8
Gene (Uniprot):rps8e
Chain IDs:YA (auth: BJ)
Chain Length:131
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWY2 Pfam ID:PF01201
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Chain IDs:ZA (auth: BK)
Chain Length:142
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ8 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rps10
Chain IDs:AB (auth: BL)
Chain Length:106
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MT22 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rps11
Chain IDs:BB (auth: BM)
Chain Length:141
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX63 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rps12
Chain IDs:CB (auth: BN)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ4 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rps13
Chain IDs:DB (auth: BO)
Chain Length:153
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUT0 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rps14
Chain IDs:EB (auth: BP)
Chain Length:54
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ7 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rps15
Chain IDs:FB (auth: BQ)
Chain Length:151
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MVD1 Pfam ID:PF08069, PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rps17
Chain IDs:GB (auth: BR)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTT7 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS17
Gene (Uniprot):rps17e
Chain IDs:HB (auth: BS)
Chain Length:71
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS42 Pfam ID:PF00833
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Chain IDs:IB (auth: BT)
Chain Length:158
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTT6
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS19
Gene (Uniprot):rps19e
Chain IDs:JB (auth: BU)
Chain Length:158
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUU6 Pfam ID:PF01090
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS24
Gene (Uniprot):rps24e
Chain IDs:KB (auth: BV)
Chain Length:128
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSX4 Pfam ID:PF01282
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SSU ribosomal protein S25E
Gene (Uniprot):Pcal_1079
Chain IDs:LB (auth: BW)
Chain Length:110
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MV37 Pfam ID:PF03297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SSU ribosomal protein S26E
Gene (Uniprot):Pcal_1091
Chain IDs:MB (auth: BX)
Chain Length:100
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MV49 Pfam ID:PF01283
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS27
Gene (Uniprot):rps27e
Chain IDs:NB (auth: BY)
Chain Length:67
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUV2 Pfam ID:PF01667
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS28
Gene (Uniprot):rps28e
Chain IDs:OB (auth: BZ)
Chain Length:77
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:B1Y9V2 Pfam ID:PF01200
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SSU ribosomal protein S30E
Gene (Uniprot):Pcal_0294
Chain IDs:PB (auth: Ba)
Chain Length:54
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSW3 Pfam ID:PF04758
Polymer Type:polypeptide(L)
Molecule:aS35
Chain IDs:QB (auth: Bb)
Chain Length:208
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
Gene (Uniprot):Pcal_2113
Chain IDs:RB (auth: Bc)
Chain Length:216
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MY11 Pfam ID:PF07754
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
6MZ D A modified residue
A2M D A modified residue
B8T D C modified residue
M7A D A modified residue
MA6 D A modified residue
OMC D C modified residue
OMG D G modified residue
OMU D U modified residue
PSU D U modified residue
Ligand Molecules
MG
SPM
ZN
Primary Citation
Structure of an archaeal ribosome reveals a divergent active site and hibernation factor.
Nat Microbiol 10 1940 1953 (2025)
PMID: 40676158 DOI: 10.1038/s41564-025-02065-w

Abstact

Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase centre (PTC), is thought to be nearly universally conserved. Here we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC. To understand how these PTC sequences fold, we determined cryo-EM structures of the 70S and 50S ribosomes to 2.4 Å and 2 Å, respectively, from the hyperthermophilic archaeon Pyrobaculum calidifontis. PTC sequence variation leads to the rearrangement of key base triples, and differences between archaeal and bacterial ribosomal proteins enable sequence variation in archaeal PTCs. Finally, we identify an archaeal ribosome hibernation factor, Dri, that differs from known bacterial and eukaryotic hibernation factors and is found in multiple archaeal phyla. Overall, this work identifies factors that regulate ribosome function in archaea and reveals a larger diversity of the most ancient sequences in the ribosome.

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Chemical

Disease

Primary Citation of related structures
9E71
9E6Q