9E7F image
Deposition Date 2024-11-01
Release Date 2024-11-20
Last Version Date 2024-11-20
Entry Detail
PDB ID:
9E7F
Keywords:
Title:
Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.53 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
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
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
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:D (auth: 4)
Chain Length:1498
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Polymer Type:polypeptide(L)
Molecule:eL42
Chain IDs:LA (auth: Ah)
Chain Length:157
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Polymer Type:polypeptide(L)
Molecule:aS35
Chain IDs:QB (auth: Bb)
Chain Length:208
Number of Molecules:1
Biological Source:Pyrobaculum calidifontis JCM 11548
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
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
Primary Citation
Structure of an Archaeal Ribosome with a Divergent Active Site
To Be Published ? ? ? (?)
Primary Citation of related structures