9E71 image
Deposition Date 2024-10-31
Release Date 2024-11-20
Last Version Date 2024-11-20
Entry Detail
PDB ID:
9E71
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome
Biological Source:
Source Organism:
Pyrobaculum calidifontis JCM 11548 (Taxon ID: 410359)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.36 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9E71 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:B (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
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:C (auth: 4)
Chain Length:1498
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rpl2
Chain IDs:D (auth: AA)
Chain Length:91
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS41 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):rpl3
Chain IDs:E (auth: AB)
Chain Length:338
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWI4 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rpl4
Chain IDs:F (auth: AC)
Chain Length:285
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWI5 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rpl5
Chain IDs:G (auth: AD)
Chain Length:52
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXP8 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rpl6
Chain IDs:H (auth: AE)
Chain Length:67
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWV5 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL8
Gene (Uniprot):rpl7ae
Chain IDs:I (auth: AF)
Chain Length:149
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTA9 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rpl13
Chain IDs:J (auth: AG)
Chain Length:186
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ7 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL13
Gene (Uniprot):rpl13e
Chain IDs:K (auth: AH)
Chain Length:91
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTP8 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rpl14
Chain IDs:L (auth: AI)
Chain Length:144
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX34 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL14
Gene (Uniprot):rpl14e
Chain IDs:M (auth: AJ), N (auth: AK)
Chain Length:103
Number of Molecules:2
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS76
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rpl15
Chain IDs:O (auth: AL)
Chain Length:156
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUZ1 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15e
Gene (Uniprot):Pcal_1666
Chain IDs:P (auth: AM)
Chain Length:189
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWR6 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rpl10e
Chain IDs:Q (auth: AN)
Chain Length:178
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXP3 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rpl18
Chain IDs:R (auth: AO)
Chain Length:205
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ3 Pfam ID:PF17144
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL18
Gene (Uniprot):rpl18e
Chain IDs:S (auth: AP)
Chain Length:122
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ6 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL19
Gene (Uniprot):rpl19e
Chain IDs:T (auth: AQ)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ4 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL20
Gene (Uniprot):rpl18a
Chain IDs:U (auth: AR)
Chain Length:78
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX77 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL21
Gene (Uniprot):rpl21e
Chain IDs:V (auth: AS)
Chain Length:99
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWX9 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rpl22
Chain IDs:W (auth: AT)
Chain Length:184
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTL6 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rpl23
Chain IDs:X (auth: AU)
Chain Length:81
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWI6 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rpl24
Chain IDs:Y (auth: AV)
Chain Length:128
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWZ8 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL24
Gene (Uniprot):rpl24e
Chain IDs:Z (auth: AW)
Chain Length:62
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTA8 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpl29
Chain IDs:AA (auth: AX)
Chain Length:79
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTL2 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpl30
Chain IDs:BA (auth: AY)
Chain Length:179
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MU87 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL30
Gene (Uniprot):rpl30e
Chain IDs:CA (auth: AZ)
Chain Length:101
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ2 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL31
Gene (Uniprot):rpl31e
Chain IDs:DA (auth: Aa)
Chain Length:91
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX75 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL32
Gene (Uniprot):rpl32e
Chain IDs:EA (auth: Ab)
Chain Length:338
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ5 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL34
Gene (Uniprot):rpl34e
Chain IDs:FA (auth: Ac)
Chain Length:285
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MV68 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL37
Gene (Uniprot):rpl37e
Chain IDs:GA (auth: Ad)
Chain Length:52
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MY38 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:LSU ribosomal protein L38E
Gene (Uniprot):Pcal_0622
Chain IDs:HA (auth: Ae)
Chain Length:67
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTT1 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL39
Gene (Uniprot):rpl39e
Chain IDs:IA (auth: Af)
Chain Length:149
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUU4 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL40
Gene (Uniprot):rpl40e
Chain IDs:JA (auth: Ag)
Chain Length:186
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX99 Pfam ID:PF01020
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL42
Chain IDs:KA (auth: Ah)
Chain Length:91
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUV1 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL43
Gene (Uniprot):rpl37ae
Chain IDs:LA (auth: Ai)
Chain Length:144
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUM7 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DJ-1/PfpI domain-containing protein
Gene (Uniprot):Pcal_0567
Chain IDs:MA (auth: Aj)
Chain Length:103
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTM7 Pfam ID:PF01965
Protein Blast
Polymer Type:polypeptide(L)
Molecule:PaREP1 domain containing protein
Gene (Uniprot):Pcal_1690
Chain IDs:NA (auth: Ak)
Chain Length:103
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWU0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS1
Gene (Uniprot):rps3ae
Chain IDs:OA (auth: BA)
Chain Length:222
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MVE0 Pfam ID:PF01015
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rps2
Chain IDs:PA (auth: BB)
Chain Length:208
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS50 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rps3
Chain IDs:QA (auth: BC)
Chain Length:216
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTL3 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rps4
Chain IDs:RA (auth: BD)
Chain Length:159
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUS9 Pfam ID:PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS4
Gene (Uniprot):rps4e
Chain IDs:SA (auth: BE)
Chain Length:237
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWZ7 Pfam ID:PF08071, PF01479, PF00900
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rps5
Chain IDs:TA (auth: BF)
Chain Length:202
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MU88 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS6
Gene (Uniprot):rps6e
Chain IDs:UA (auth: BG)
Chain Length:151
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUD0 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rps7
Chain IDs:VA (auth: BH)
Chain Length:223
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS29 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rps8
Chain IDs:WA (auth: BI)
Chain Length:130
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ6 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS8
Gene (Uniprot):rps8e
Chain IDs:XA (auth: BJ)
Chain Length:131
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MWY2 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rps9
Chain IDs:YA (auth: BK)
Chain Length:142
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ8 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rps10
Chain IDs:ZA (auth: BL)
Chain Length:106
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MT22 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rps11
Chain IDs:AB (auth: BM)
Chain Length:141
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MX63 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rps12
Chain IDs:BB (auth: BN)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MXZ4 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rps13
Chain IDs:CB (auth: BO)
Chain Length:153
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUT0 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rps14
Chain IDs:DB (auth: BP)
Chain Length:54
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSJ7 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rps15
Chain IDs:EB (auth: BQ)
Chain Length:151
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MVD1 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rps17
Chain IDs:FB (auth: BR)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTT7 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS17
Gene (Uniprot):rps17e
Chain IDs:GB (auth: BS)
Chain Length:71
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MS42 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rps19
Chain IDs:HB (auth: BT)
Chain Length:158
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MTT6 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS19
Gene (Uniprot):rps19e
Chain IDs:IB (auth: BU)
Chain Length:158
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUU6 Pfam ID:PF01090
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS24
Gene (Uniprot):rps24e
Chain IDs:JB (auth: BV)
Chain Length:128
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSX4 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SSU ribosomal protein S25E
Gene (Uniprot):Pcal_1079
Chain IDs:KB (auth: BW)
Chain Length:110
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MV37 Pfam ID:PF03297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SSU ribosomal protein S26E
Gene (Uniprot):Pcal_1091
Chain IDs:LB (auth: BX)
Chain Length:100
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MV49 Pfam ID:PF01283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS27
Gene (Uniprot):rps27e
Chain IDs:MB (auth: BY)
Chain Length:67
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MUV2 Pfam ID:PF01667
Polymer Type:polypeptide(L)
Molecule:eS28
Chain IDs:NB (auth: BZ)
Chain Length:77
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SSU ribosomal protein S30E
Gene (Uniprot):Pcal_0294
Chain IDs:OB (auth: Ba)
Chain Length:222
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
UniProt ID:A3MSW3 Pfam ID:PF04758
Polymer Type:polypeptide(L)
Molecule:aS35
Chain IDs:PB (auth: Bb)
Chain Length:208
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
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:QB (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 C A modified residue
A2M C A modified residue
B8T C C modified residue
M7A C A modified residue
MA6 C A modified residue
OMC C C modified residue
OMG C G modified residue
OMU C U modified residue
PSU C U modified residue
Ligand Molecules
MG
SPM
ZN
Primary Citation
Structure of an Archaeal Ribosome with a Divergent Active Site
To Be Published ? ? ? (?)
Primary Citation of related structures
9E6Q