6RM3

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

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

(2019) Nat Microbiol 4: 1798-1804

  • DOI: 10.1038/s41564-019-0514-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance 1-3 , and are significant opportunistic parasites of humans 4 . They are characterized by having a spec ...

    Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance 1-3 , and are significant opportunistic parasites of humans 4 . They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle 5 , rudimentary mitochondria and the smallest known eukaryotic genomes 5-7 . Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome 8-10 . 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.


    Organizational Affiliation

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
uS2SA0264Vairimorpha necatrixMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
uL15LAA148Vairimorpha necatrixMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
eS26SAA104Vairimorpha necatrixMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
uL3LB0384Vairimorpha necatrixMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
eS1SB0237Vairimorpha necatrixMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
eL29LBB55Vairimorpha necatrixMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
eS27SBB94Vairimorpha necatrixMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uL4LC0334Vairimorpha necatrixMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
eL30LCC108Vairimorpha necatrixMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
eS28SCC67Vairimorpha necatrixMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uL18LD0295Vairimorpha necatrixMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uS3SD0215Vairimorpha necatrixMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
uS14SDD68Vairimorpha necatrixMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL6LE0172Vairimorpha necatrixMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eS4SE0262Vairimorpha necatrixMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
eL32LEE139Vairimorpha necatrixMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
eS30SEE60Vairimorpha necatrixMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uS7SF0189Vairimorpha necatrixMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
eL33LFF98Vairimorpha necatrixMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
eS31SFF151Vairimorpha necatrixMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eL8LG0200Vairimorpha necatrixMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eS6SG0217Vairimorpha necatrixMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RACK1SGG337Vairimorpha necatrixMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
uL6LH0186Vairimorpha necatrixMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eS7SH0161Vairimorpha necatrixMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
uL29LHH122Vairimorpha necatrixMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
uL16LI0217Vairimorpha necatrixMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
eS8SI0166Vairimorpha necatrixMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL36LII95Vairimorpha necatrixMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
uS4SJ0189Vairimorpha necatrixMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
eL37LJJ93Vairimorpha necatrixMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
uS17SL0158Vairimorpha necatrixMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eL39LLL52Vairimorpha necatrixMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
eL14LM0105Vairimorpha necatrixMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
eL40LMM127Vairimorpha necatrixMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
uS15SN0149Vairimorpha necatrixMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
MDF2LNN160Vairimorpha necatrixMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
MDF1SNN168Vairimorpha necatrixMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
uL13LO0192Vairimorpha necatrixMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
uS11SO0135Vairimorpha necatrixMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
eL42LOO103Vairimorpha necatrixMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
uL22LP0169Vairimorpha necatrixMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
uS19SP0143Vairimorpha necatrixMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
eL43LPP89Vairimorpha necatrixMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
eL18LQ0193Vairimorpha necatrixMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
uS9SQ0155Vairimorpha necatrixMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
eL19LR0175Vairimorpha necatrixMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
eS17SR0119Vairimorpha necatrixMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
uS13SS0160Vairimorpha necatrixMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
eL21LT0160Vairimorpha necatrixMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
eL22LU0107Vairimorpha necatrixMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
uS10SU0101Vairimorpha necatrixMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uL14LV0146Vairimorpha necatrixMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
eL24LW091Vairimorpha necatrixMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
uS8SW0127Vairimorpha necatrixMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
uL23LX0102Vairimorpha necatrixMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
uS12SX0140Vairimorpha necatrixMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
msL1LXX73Vairimorpha necatrixMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
uL24LY0139Vairimorpha necatrixMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
eS25SZ0123Vairimorpha necatrixMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
eS10SK099Vairimorpha necatrixMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
uS5SC0237Vairimorpha necatrixMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL31LDD111Vairimorpha necatrixMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uL30LF0239Vairimorpha necatrixMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eL34LGG106Vairimorpha necatrixMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
uL2LA0237Vairimorpha necatrixMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
uL5LJ0171Vairimorpha necatrixMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL13LL0162Vairimorpha necatrixMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
eS12SM0131Vairimorpha necatrixMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
eL15LN0204Vairimorpha necatrixMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
eL20LS0180Vairimorpha necatrixMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
eS19ST0133Vairimorpha necatrixMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
eS21SV067Vairimorpha necatrixMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
eS24SY0133Vairimorpha necatrixMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
eL27LZ0126Vairimorpha necatrixMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAS601244Vairimorpha necatrix

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Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNAL70119Vairimorpha necatrix

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Entity ID: 78
MoleculeChainsLengthOrganism
23S rRNAL502484Vairimorpha necatrix
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
LGG, LJJ, LMM, LOO, LPP, SAA, SBB, SDD, SNN
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
L50, L70, LJJ, LV0, S60
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1DP2GM123459
Swiss National Science FoundationSwitzerland155515

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references