ISDA

Deposition Date 2020-07-21

Release Date 2020-11-04

Last Version Date 2024-05-01

Entry Detail

PDB ID:

6ZU5

Keywords:

RIBOSOME

Title:

Structure of the Paranosema locustae ribosome in complex with Lso2

Biological Source:

Source Organism:

Paranosema locustae (Taxon ID: 235221)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:A (auth: L50)
Chain Length:2639
Number of Molecules:1
Biological Source:Paranosema locustae

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

Polymer Type:polypeptide(L)
Molecule:uL2
Chain IDs:C (auth: LA0)
Chain Length:247
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL15
Chain IDs:D (auth: LAA)
Chain Length:155
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL3
Chain IDs:E (auth: LB0)
Chain Length:385
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL29
Chain IDs:F (auth: LBB)
Chain Length:64
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL4
Chain IDs:G (auth: LC0)
Chain Length:330
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL30
Chain IDs:H (auth: LCC)
Chain Length:108
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL18
Chain IDs:I (auth: LD0)
Chain Length:266
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL31
Chain IDs:J (auth: LDD)
Chain Length:109
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL6
Chain IDs:K (auth: LE0)
Chain Length:180
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL32
Chain IDs:L (auth: LEE)
Chain Length:132
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL30
Chain IDs:M (auth: LF0)
Chain Length:254
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL33
Chain IDs:N (auth: LFF)
Chain Length:108
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL8
Chain IDs:O (auth: LG0)
Chain Length:216
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL34
Chain IDs:P (auth: LGG)
Chain Length:113
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL6
Chain IDs:Q (auth: LH0)
Chain Length:186
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL29
Chain IDs:R (auth: LHH)
Chain Length:126
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL16
Chain IDs:S (auth: LI0)
Chain Length:218
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL36
Chain IDs:T (auth: LII)
Chain Length:98
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL5
Chain IDs:U (auth: LJ0)
Chain Length:174
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL37
Chain IDs:V (auth: LJJ)
Chain Length:95
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL13
Chain IDs:W (auth: LL0)
Chain Length:166
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL39
Chain IDs:X (auth: LLL)
Chain Length:51
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL14
Chain IDs:Y (auth: LM0)
Chain Length:108
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL40
Chain IDs:Z (auth: LMM)
Chain Length:132
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL15
Chain IDs:AA (auth: LN0)
Chain Length:204
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:Lso2
Chain IDs:BA (auth: LNN)
Chain Length:77
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL13
Chain IDs:CA (auth: LO0)
Chain Length:198
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL42
Chain IDs:DA (auth: LOO)
Chain Length:112
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL22
Chain IDs:EA (auth: LP0)
Chain Length:171
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL43
Chain IDs:FA (auth: LPP)
Chain Length:86
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL18
Chain IDs:GA (auth: LQ0)
Chain Length:178
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL19
Chain IDs:HA (auth: LR0)
Chain Length:166
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL20
Chain IDs:IA (auth: LS0)
Chain Length:175
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL21
Chain IDs:JA (auth: LT0)
Chain Length:160
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL22
Chain IDs:KA (auth: LU0)
Chain Length:114
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL14
Chain IDs:LA (auth: LV0)
Chain Length:140
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL24
Chain IDs:MA (auth: LW0)
Chain Length:133
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL23
Chain IDs:NA (auth: LX0)
Chain Length:106
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uL24
Chain IDs:OA (auth: LY0)
Chain Length:140
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eL27
Chain IDs:PA (auth: LZ0)
Chain Length:127
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:QA (auth: S60)
Chain Length:1400
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS2
Chain IDs:RA (auth: SA0)
Chain Length:242
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS26
Chain IDs:SA (auth: SAA)
Chain Length:104
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS1
Chain IDs:TA (auth: SB0)
Chain Length:230
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS27
Chain IDs:UA (auth: SBB)
Chain Length:86
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS5
Chain IDs:VA (auth: SC0)
Chain Length:255
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS28
Chain IDs:WA (auth: SCC)
Chain Length:65
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS3
Chain IDs:XA (auth: SD0)
Chain Length:217
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS14
Chain IDs:YA (auth: SDD)
Chain Length:63
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS4
Chain IDs:ZA (auth: SE0)
Chain Length:267
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS30
Chain IDs:AB (auth: SEE)
Chain Length:60
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS7
Chain IDs:BB (auth: SF0)
Chain Length:195
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS6
Chain IDs:CB (auth: SG0)
Chain Length:222
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:RACK1
Chain IDs:DB (auth: SGG)
Chain Length:330
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS7
Chain IDs:EB (auth: SH0)
Chain Length:176
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS8
Chain IDs:FB (auth: SI0)
Chain Length:175
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS4
Chain IDs:GB (auth: SJ0)
Chain Length:187
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS10
Chain IDs:HB (auth: SK0)
Chain Length:102
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS17
Chain IDs:IB (auth: SL0)
Chain Length:160
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS15
Chain IDs:JB (auth: SN0)
Chain Length:146
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS11
Chain IDs:KB (auth: SO0)
Chain Length:135
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS19
Chain IDs:LB (auth: SP0)
Chain Length:146
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS9
Chain IDs:MB (auth: SQ0)
Chain Length:145
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS17
Chain IDs:NB (auth: SR0)
Chain Length:123
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS13
Chain IDs:OB (auth: SS0)
Chain Length:161
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS19
Chain IDs:PB (auth: ST0)
Chain Length:141
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS10
Chain IDs:QB (auth: SU0)
Chain Length:111
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS21
Chain IDs:RB (auth: SV0)
Chain Length:66
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS8
Chain IDs:SB (auth: SW0)
Chain Length:127
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:uS12
Chain IDs:TB (auth: SX0)
Chain Length:140
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS24
Chain IDs:UB (auth: SY0)
Chain Length:133
Number of Molecules:1
Biological Source:Paranosema locustae

Polymer Type:polypeptide(L)
Molecule:eS25
Chain IDs:VB (auth: SZ0)
Chain Length:126
Number of Molecules:1
Biological Source:Paranosema locustae

Ligand Molecules

AMP

Primary Citation

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome.

Ehrenbolger, K, Jespersen, N, Sharma, H, Sokolova, Y.Y, Tokarev, Y.S, Vossbrinck, C.R, Barandun, J.Show

Plos Biol. 18 e3000958 e3000958 (2020)

PMID: 33125369 DOI: 10.1371/journal.pbio.3000958

Abstact

Assembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic microsporidia, conservation of energy via ribosomal hibernation and recycling is critical. The mechanisms by which hibernation is achieved in microsporidia, however, remain poorly understood. Here, we present the cryo-electron microscopy structure of the ribosome from Paranosema locustae spores, bound by the conserved eukaryotic hibernation and recycling factor Lso2. The microsporidian Lso2 homolog adopts a V-shaped conformation to bridge the mRNA decoding site and the large subunit tRNA binding sites, providing a reversible ribosome inactivation mechanism. Although microsporidian ribosomes are highly compacted, the P. locustae ribosome retains several rRNA segments absent in other microsporidia, and represents an intermediate state of rRNA reduction. In one case, the near complete reduction of an expansion segment has resulted in a single bound nucleotide, which may act as an architectural co-factor to stabilize a protein-protein interface. The presented structure highlights the reductive evolution in these emerging pathogens and sheds light on a conserved mechanism for eukaryotic ribosome hibernation.

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Protein

Chemical

Disease

Primary Citation of related structures