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: 3
MoleculeChainsSequence LengthOrganismDetails
uL2
LA0
237Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
uS2
SA0
264Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
uL15
LAA
148Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
eS26
SAA
104Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
uL3
LB0
384Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
eS1
SB0
237Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
eL29
LBB
55Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
eS27
SBB
94Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uL4
LC0
334Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
uS5
SC0
237Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
eL30
LCC
108Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
eS28
SCC
67Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uL18
LD0
295Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uS3
SD0
215Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL31
LDD
111Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
uS14
SDD
68Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL6
LE0
172Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eS4
SE0
262Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
eL32
LEE
139Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
eS30
SEE
60Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uL30
LF0
239Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uS7
SF0
189Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
eL33
LFF
98Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
eS31
SFF
151Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eL8
LG0
200Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eS6
SG0
217Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eL34
LGG
106Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RACK1
SGG
337Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
uL6
LH0
186Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eS7
SH0
161Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
uL29
LHH
122Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
uL16
LI0
217Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
eS8
SI0
166Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL36
LII
95Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
uL5
LJ0
171Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
uS4
SJ0
189Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
eL37
LJJ
93Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL13
LL0
162Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
uS17
SL0
158Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eL39
LLL
52Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
eL14
LM0
105Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
eL40
LMM
127Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
eS12
SM0
131Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
eL15
LN0
204Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
uS15
SN0
149Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
MDF2
LNN
160Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
MDF1
SNN
168Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
uL13
LO0
192Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
uS11
SO0
135Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
eL42
LOO
103Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
uL22
LP0
169Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
uS19
SP0
143Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
eL43
LPP
89Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
eL18
LQ0
193Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
uS9
SQ0
155Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
eL19
LR0
175Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
eS17
SR0
119Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
eL20
LS0
180Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
uS13
SS0
160Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
eL21
LT0
160Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
eS19
ST0
133Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
eL22
LU0
107Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
uS10
SU0
101Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uL14
LV0
146Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
eS21
SV0
67Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
eL24
LW0
91Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
uS8
SW0
127Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
uL23
LX0
102Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
uS12
SX0
140Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
msL1
LXX
73Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
uL24
LY0
139Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
eS24
SY0
133Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
eL27
LZ0
126Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
eS25
SZ0
123Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
eS10
SK0
99Vairimorpha necatrixMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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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

View Full Validation Report



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