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- PDB-6zu5: Structure of the Paranosema locustae ribosome in complex with Lso2 -

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Basic information

Entry
Database: PDB / ID: 6zu5
TitleStructure of the Paranosema locustae ribosome in complex with Lso2
Components
  • 18S rRNA18S ribosomal RNA
  • 25S rRNA
  • 5S rRNA5S ribosomal RNA
  • Lso2
  • RACK1Receptor for activated C kinase 1
  • eL13
  • eL14
  • eL15List of Subaru engines
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL27
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL36
  • eL37
  • eL39
  • eL40
  • eL42
  • eL43
  • eL6
  • eL8
  • eS1
  • eS10
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS4
  • eS6
  • eS7
  • eS8
  • uL13
  • uL14
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL23
  • uL24
  • uL29
  • uL3
  • uL30
  • uL4
  • uL5
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / Microsporidia / Pathogen / Hibernation / Genome Compaction
Function / homologyADENOSINE MONOPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesParanosema locustae (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsEhrenbolger, K. / Jespersen, N. / Sharma, H. / Sokolova, Y.Y. / Tokarev, Y.S. / Vossbrinck, C.R. / Barandun, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2019-02011 Sweden
CitationJournal: PLoS Biol / Year: 2020
Title: Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome.
Authors: Kai Ehrenbolger / Nathan Jespersen / Himanshu Sharma / Yuliya Y Sokolova / Yuri S Tokarev / Charles R Vossbrinck / Jonas Barandun /
Abstract: Assembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic ...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.
History
DepositionJul 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-11437
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L50: 25S rRNA
L70: 5S rRNA
LA0: uL2
LAA: uL15
LB0: uL3
LBB: eL29
LC0: uL4
LCC: eL30
LD0: uL18
LDD: eL31
LE0: eL6
LEE: eL32
LF0: uL30
LFF: eL33
LG0: eL8
LGG: eL34
LH0: uL6
LHH: uL29
LI0: uL16
LII: eL36
LJ0: uL5
LJJ: eL37
LL0: eL13
LLL: eL39
LM0: eL14
LMM: eL40
LN0: eL15
LNN: Lso2
LO0: uL13
LOO: eL42
LP0: uL22
LPP: eL43
LQ0: eL18
LR0: eL19
LS0: eL20
LT0: eL21
LU0: eL22
LV0: uL14
LW0: eL24
LX0: uL23
LY0: uL24
LZ0: eL27
S60: 18S rRNA
SA0: uS2
SAA: eS26
SB0: eS1
SBB: eS27
SC0: uS5
SCC: eS28
SD0: uS3
SDD: uS14
SE0: eS4
SEE: eS30
SF0: uS7
SG0: eS6
SGG: RACK1
SH0: eS7
SI0: eS8
SJ0: uS4
SK0: eS10
SL0: uS17
SN0: uS15
SO0: uS11
SP0: uS19
SQ0: uS9
SR0: eS17
SS0: uS13
ST0: eS19
SU0: uS10
SV0: eS21
SW0: uS8
SX0: uS12
SY0: eS24
SZ0: eS25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,628,109262
Polymers2,622,88874
Non-polymers5,221188
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules L50L70S60

#1: RNA chain 25S rRNA


Mass: 854380.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38434.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#43: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 456967.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)

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Protein , 71 types, 71 molecules LA0LAALB0LBBLC0LCCLD0LDDLE0LEELF0LFFLG0LGGLH0LHHLI0LIILJ0LJJLL0LLLLM0LMMLN0LNNLO0LOOLP0LPP...

#3: Protein uL2


Mass: 26693.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#4: Protein uL15


Mass: 17532.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#5: Protein uL3


Mass: 43599.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#6: Protein eL29


Mass: 7622.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#7: Protein uL4


Mass: 37110.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#8: Protein eL30


Mass: 11819.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#9: Protein uL18


Mass: 31082.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#10: Protein eL31


Mass: 12772.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#11: Protein eL6


Mass: 20550.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#12: Protein eL32 / CD59


Mass: 15613.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#13: Protein uL30


Mass: 30087.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#14: Protein eL33


Mass: 12309.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#15: Protein eL8


Mass: 24884.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#16: Protein eL34 /


Mass: 12878.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#17: Protein uL6


Mass: 21066.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#18: Protein uL29


Mass: 15352.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#19: Protein uL16


Mass: 24798.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#20: Protein eL36


Mass: 11431.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#21: Protein uL5


Mass: 19817.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#22: Protein eL37


Mass: 10792.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#23: Protein eL13


Mass: 19552.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#24: Protein eL39


Mass: 6467.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#25: Protein eL14


Mass: 12682.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#26: Protein eL40


Mass: 14495.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#27: Protein eL15 / List of Subaru engines


Mass: 23671.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#28: Protein Lso2


Mass: 9415.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#29: Protein uL13


Mass: 23119.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#30: Protein eL42


Mass: 13239.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#31: Protein uL22


Mass: 19492.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#32: Protein eL43


Mass: 9214.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#33: Protein eL18


Mass: 20016.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#34: Protein eL19


Mass: 19522.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#35: Protein eL20


Mass: 20855.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#36: Protein eL21 /


Mass: 18688.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#37: Protein eL22


Mass: 13247.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#38: Protein uL14


Mass: 15257.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#39: Protein eL24


Mass: 15209.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#40: Protein uL23


Mass: 11872.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#41: Protein uL24


Mass: 16620.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#42: Protein eL27


Mass: 14285.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#44: Protein uS2


Mass: 27336.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#45: Protein eS26


Mass: 11985.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#46: Protein eS1


Mass: 26208.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#47: Protein eS27


Mass: 9923.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#48: Protein uS5


Mass: 28251.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#49: Protein eS28


Mass: 7325.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#50: Protein uS3


Mass: 24682.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#51: Protein uS14


Mass: 7481.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#52: Protein eS4


Mass: 30011.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#53: Protein eS30


Mass: 7010.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#54: Protein uS7


Mass: 21633.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#55: Protein eS6


Mass: 25832.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#56: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35507.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#57: Protein eS7


Mass: 20213.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#58: Protein eS8


Mass: 20073.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#59: Protein uS4


Mass: 21702.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#60: Protein eS10


Mass: 11604.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#61: Protein uS17


Mass: 18735.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#62: Protein uS15


Mass: 16639.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#63: Protein uS11


Mass: 14354.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#64: Protein uS19


Mass: 16537.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#65: Protein uS9


Mass: 16499.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#66: Protein eS17


Mass: 14702.942 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#67: Protein uS13


Mass: 18093.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#68: Protein eS19


Mass: 16191.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#69: Protein uS10


Mass: 12699.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#70: Protein eS21


Mass: 7380.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#71: Protein uS8


Mass: 14369.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#72: Protein uS12


Mass: 15789.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#73: Protein eS24


Mass: 15866.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)
#74: Protein eS25


Mass: 13719.942 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paranosema locustae (fungus)

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Non-polymers , 3 types, 188 molecules

#75: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 179 / Source method: obtained synthetically / Formula: Mg
#76: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#77: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lso2 bound to the ribosome of Paranosema locustae / Type: RIBOSOME / Entity ID: #1-#74 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Paranosema locustae (fungus)
Buffer solutionpH: 7.5
Details: 30 mM Tris-HCl, pH 7.5, 25 mM KCl, 5 mM magnesium acetate, 1 mM DTT, 1 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 28.6 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4RELION3.1CTF correctionfor final refinement
5CTFFIND4.1.13CTF correctionfor initial CTF estimation
8Coot0.8.9.2model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.14-3260model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 320669
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124947 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model buildingPDB-ID: 4V88

4v88

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