ISDA: 6RM3

Deposition Date 2019-05-05

Release Date 2019-07-10

Last Version Date 2024-07-10

Entry Detail

PDB ID:

6RM3

Keywords:

RIBOSOME

Title:

Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome

Biological Source:

Source Organism:

Vairimorpha necatrix (Taxon ID: 6039)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:ZB (auth: L50)
Chain Length:2484
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B (auth: L70)
Chain Length:119
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL2
Chain IDs:C (auth: LA0)
Chain Length:237
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL15
Chain IDs:E (auth: LAA)
Chain Length:148
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL3
Chain IDs:G (auth: LB0)
Chain Length:384
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL29
Chain IDs:I (auth: LBB)
Chain Length:55
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL4
Chain IDs:K (auth: LC0)
Chain Length:334
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL30
Chain IDs:M (auth: LCC)
Chain Length:108
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL18
Chain IDs:O (auth: LD0)
Chain Length:295
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL31
Chain IDs:Q (auth: LDD)
Chain Length:111
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL6
Chain IDs:S (auth: LE0)
Chain Length:172
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL32
Chain IDs:U (auth: LEE)
Chain Length:139
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL30
Chain IDs:W (auth: LF0)
Chain Length:239
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL33
Chain IDs:Y (auth: LFF)
Chain Length:98
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL8
Chain IDs:AA (auth: LG0)
Chain Length:200
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL34
Chain IDs:CA (auth: LGG)
Chain Length:106
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL6
Chain IDs:EA (auth: LH0)
Chain Length:186
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL29
Chain IDs:GA (auth: LHH)
Chain Length:122
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL16
Chain IDs:HA (auth: LI0)
Chain Length:217
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL36
Chain IDs:JA (auth: LII)
Chain Length:95
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL5
Chain IDs:KA (auth: LJ0)
Chain Length:171
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL37
Chain IDs:MA (auth: LJJ)
Chain Length:93
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL13
Chain IDs:NA (auth: LL0)
Chain Length:162
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL39
Chain IDs:PA (auth: LLL)
Chain Length:52
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL14
Chain IDs:QA (auth: LM0)
Chain Length:105
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL40
Chain IDs:RA (auth: LMM)
Chain Length:127
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL15
Chain IDs:TA (auth: LN0)
Chain Length:204
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:MDF2
Chain IDs:VA (auth: LNN)
Chain Length:160
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL13
Chain IDs:XA (auth: LO0)
Chain Length:192
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL42
Chain IDs:ZA (auth: LOO)
Chain Length:103
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL22
Chain IDs:AB (auth: LP0)
Chain Length:169
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL43
Chain IDs:CB (auth: LPP)
Chain Length:89
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL18
Chain IDs:DB (auth: LQ0)
Chain Length:193
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL19
Chain IDs:FB (auth: LR0)
Chain Length:175
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL20
Chain IDs:HB (auth: LS0)
Chain Length:180
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL21
Chain IDs:JB (auth: LT0)
Chain Length:160
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL22
Chain IDs:LB (auth: LU0)
Chain Length:107
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL14
Chain IDs:NB (auth: LV0)
Chain Length:146
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL24
Chain IDs:PB (auth: LW0)
Chain Length:91
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL23
Chain IDs:RB (auth: LX0)
Chain Length:102
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:msL1
Chain IDs:TB (auth: LXX)
Chain Length:73
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uL24
Chain IDs:UB (auth: LY0)
Chain Length:139
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eL27
Chain IDs:WB (auth: LZ0)
Chain Length:126
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: S60)
Chain Length:1244
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS2
Chain IDs:D (auth: SA0)
Chain Length:264
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS26
Chain IDs:F (auth: SAA)
Chain Length:104
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS1
Chain IDs:H (auth: SB0)
Chain Length:237
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS27
Chain IDs:J (auth: SBB)
Chain Length:94
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS5
Chain IDs:L (auth: SC0)
Chain Length:237
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS28
Chain IDs:N (auth: SCC)
Chain Length:67
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS3
Chain IDs:P (auth: SD0)
Chain Length:215
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS14
Chain IDs:R (auth: SDD)
Chain Length:68
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS4
Chain IDs:T (auth: SE0)
Chain Length:262
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS30
Chain IDs:V (auth: SEE)
Chain Length:60
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS7
Chain IDs:X (auth: SF0)
Chain Length:189
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS31
Chain IDs:Z (auth: SFF)
Chain Length:151
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS6
Chain IDs:BA (auth: SG0)
Chain Length:217
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:RACK1
Chain IDs:DA (auth: SGG)
Chain Length:337
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS7
Chain IDs:FA (auth: SH0)
Chain Length:161
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS8
Chain IDs:IA (auth: SI0)
Chain Length:166
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS4
Chain IDs:LA (auth: SJ0)
Chain Length:189
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS10
Chain IDs:YB (auth: SK0)
Chain Length:99
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS17
Chain IDs:OA (auth: SL0)
Chain Length:158
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS12
Chain IDs:SA (auth: SM0)
Chain Length:131
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS15
Chain IDs:UA (auth: SN0)
Chain Length:149
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:MDF1
Chain IDs:WA (auth: SNN)
Chain Length:168
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS11
Chain IDs:YA (auth: SO0)
Chain Length:135
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS19
Chain IDs:BB (auth: SP0)
Chain Length:143
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS9
Chain IDs:EB (auth: SQ0)
Chain Length:155
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS17
Chain IDs:GB (auth: SR0)
Chain Length:119
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS13
Chain IDs:IB (auth: SS0)
Chain Length:160
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS19
Chain IDs:KB (auth: ST0)
Chain Length:133
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS10
Chain IDs:MB (auth: SU0)
Chain Length:101
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS21
Chain IDs:OB (auth: SV0)
Chain Length:67
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS8
Chain IDs:QB (auth: SW0)
Chain Length:127
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:uS12
Chain IDs:SB (auth: SX0)
Chain Length:140
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS24
Chain IDs:VB (auth: SY0)
Chain Length:133
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Polymer Type:polypeptide(L)
Molecule:eS25
Chain IDs:XB (auth: SZ0)
Chain Length:123
Number of Molecules:1
Biological Source:Vairimorpha necatrix

Ligand Molecules

Primary Citation

Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.

Barandun, J, Hunziker, M, Vossbrinck, C.R, Klinge, S.Show

Nat Microbiol 4 1798 1804 (2019)

PMID: 31332387 DOI: 10.1038/s41564-019-0514-6

Abstact

Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance1-3, and are significant opportunistic parasites of humans4. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle5, rudimentary mitochondria and the smallest known eukaryotic genomes5-7. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome8-10. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.

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Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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