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- PDB-9fi8: SSU(head) structure derived from the SSU sample of the mitoriboso... -

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Basic information

Entry
Database: PDB / ID: 9fi8
TitleSSU(head) structure derived from the SSU sample of the mitoribosome from T. gondii.
Components
  • (Ribosomal protein ...) x 2
  • (Small ribosomal subunit protein ...) x 2
  • 30S ribosomal protein S5, putative
  • AP2 domain transcription factor AP2IX-6
  • Acylphosphatase-like domain-containing protein
  • DNA double-strand break repair rad50 ATPase
  • RAP domain-containing protein
  • RNA19-SSU
  • RNA5-SSU
  • RNA9-SSU
  • SSUB-SSU
  • SSUD
  • mS141
  • mS149
  • mS151
  • mS152
  • mS155
  • mS157
  • mS159
  • mS161
  • mS33/mS27
  • ms158
  • uS10m
  • ulr22
  • ulr23
  • ulr24
KeywordsRIBOSOME / Complex / translation / rRNA
Function / homology
Function and homology information


mitochondrial small ribosomal subunit / small ribosomal subunit / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding
Similarity search - Function
Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal ...Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S14, putative / Acylphosphatase-like domain-containing protein ...: / : / : / RNA / RNA (> 10) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S14, putative / Acylphosphatase-like domain-containing protein / Uncharacterized protein / Uncharacterized protein / DNA double-strand break repair rad50 ATPase / Uncharacterized protein / RAP domain-containing protein / Uncharacterized protein / 30S ribosomal protein S5, putative / Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein / Ribosomal protein S9, putative / Uncharacterized protein / Uncharacterized protein / AP2 domain transcription factor AP2IX-6 / Small ribosomal subunit protein mS29 / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRocha, R.E.O. / Barua, S. / Boissier, F. / Nguyen, T.T. / Hashem, Y.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101088541European Union
CitationJournal: Nat Commun / Year: 2024
Title: Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine.
Authors: Chaoyue Wang / Sari Kassem / Rafael Eduardo Oliveira Rocha / Pei Sun / Tan-Trung Nguyen / Joachim Kloehn / Xianyong Liu / Lorenzo Brusini / Alessandro Bonavoglia / Sramona Barua / Fanny ...Authors: Chaoyue Wang / Sari Kassem / Rafael Eduardo Oliveira Rocha / Pei Sun / Tan-Trung Nguyen / Joachim Kloehn / Xianyong Liu / Lorenzo Brusini / Alessandro Bonavoglia / Sramona Barua / Fanny Boissier / Mayara Lucia Del Cistia / Hongjuan Peng / Xinming Tang / Fujie Xie / Zixuan Wang / Oscar Vadas / Xun Suo / Yaser Hashem / Dominique Soldati-Favre / Yonggen Jia /
Abstract: The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, ...The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, leaving only three protein-coding genes and highly fragmented mitoribosomal rRNAs, raising challenging questions about mitoribosome composition, assembly and structure. Our study reveals how Toxoplasma gondii assembles over 40 mt-rRNA fragments using exclusively nuclear-encoded mitoribosomal proteins and three lineage-specific families of RNA-binding proteins. Among these are four proteins from the Apetala2/Ethylene Response Factor (AP2/ERF) family, originally known as transcription factors in plants and Apicomplexa, now repurposed as essential mitoribosome components. Cryo-EM analysis of the mitoribosome structure demonstrates how these AP2 proteins function as RNA binders to maintain mitoribosome integrity. The mitoribosome is also decorated with members of lineage-specific RNA-binding proteins belonging to RAP (RNA-binding domain abundant in Apicomplexa) proteins and HPR (heptatricopeptide repeat) families, highlighting the unique adaptations of these parasites. Solving the molecular puzzle of apicomplexan mitoribosome could inform the development of therapeutic strategies targeting organellar translation.
History
DepositionMay 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
HA: Small ribosomal subunit protein mS29,mS29(DAP3)
HB: Ribosomal protein S9, putative
HC: uS10m
HD: Ribosomal protein S14, putative
HE: mS157
HF: DNA double-strand break repair rad50 ATPase
HG: mS149
HH: ms158
HI: mS151
HJ: 30S ribosomal protein S5, putative
HK: mS155
HL: mS159
HM: RAP domain-containing protein
HN: mS161
HO: mS152
HP: Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein
HQ: mS141
HR: AP2 domain transcription factor AP2IX-6
HS: Acylphosphatase-like domain-containing protein
HT: mS33/mS27
bN: SSUB-SSU
hB: SSUD
hD: ulr22
hG: RNA9-SSU
hL: RNA5-SSU
hM: ulr23
hR: RNA19-SSU
hS: ulr24


Theoretical massNumber of molelcules
Total (without water)656,68328
Polymers656,68328
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Small ribosomal subunit protein ... , 2 types, 2 molecules HAHP

#1: Protein Small ribosomal subunit protein mS29,mS29(DAP3)


Mass: 57323.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GCU6
#16: Protein Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein


Mass: 27990.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F5W4

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Ribosomal protein ... , 2 types, 2 molecules HBHD

#2: Protein Ribosomal protein S9, putative


Mass: 17637.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F943
#4: Protein Ribosomal protein S14, putative


Mass: 12011.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YWE1

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Protein , 15 types, 15 molecules HCHEHFHGHHHIHJHKHLHMHOHQHRHSHT

#3: Protein uS10m


Mass: 26630.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F4G4
#5: Protein mS157


Mass: 18921.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8G684
#6: Protein DNA double-strand break repair rad50 ATPase


Mass: 40243.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8ETI9
#7: Protein mS149


Mass: 10301.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YMK3
#8: Protein ms158


Mass: 10757.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GU15
#9: Protein mS151


Mass: 17023.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YQQ1
#10: Protein 30S ribosomal protein S5, putative


Mass: 49936.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F5G8
#11: Protein mS155


Mass: 14861.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8EW95
#12: Protein mS159


Mass: 9367.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YYH5
#13: Protein RAP domain-containing protein


Mass: 66455.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F0U0
#15: Protein mS152


Mass: 19762.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GML4
#17: Protein mS141


Mass: 82984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8G3J1
#18: Protein AP2 domain transcription factor AP2IX-6


Mass: 20114.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8G8E7
#19: Protein Acylphosphatase-like domain-containing protein


Mass: 14236.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YXT1
#20: Protein mS33/mS27


Mass: 46515.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YG13

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Protein/peptide , 1 types, 1 molecules HN

#14: Protein/peptide mS161


Mass: 3360.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8ERU3

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RNA chain , 8 types, 8 molecules bNhBhDhGhLhMhRhS

#21: RNA chain SSUB-SSU


Mass: 18433.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: GenBank: 1867442358
#22: RNA chain SSUD


Mass: 18120.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: GenBank: 1867442364
#23: RNA chain ulr22


Mass: 4547.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#24: RNA chain RNA9-SSU


Mass: 21695.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: GenBank: 1867442351
#25: RNA chain RNA5-SSU


Mass: 10621.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#26: RNA chain ulr23


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#27: RNA chain RNA19-SSU


Mass: 8653.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#28: RNA chain ulr24


Mass: 5159.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

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Details

Has protein modificationN

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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: SSU head structure sample of the mitoribosome from T. gondii.
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Toxoplasma gondii (eukaryote) / Cellular location: Cytoplasm / Organelle: Mitochondria
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blotting force 5, blotting time 2.5 seconds.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 95 K / Temperature (min): 90 K
Image recordingAverage exposure time: 6 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9524
Image scansSampling size: 6.35 µm / Width: 4096 / Height: 4096 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.1particle selection
2SerialEM4.1image acquisition
4CTFFIND4CTF correction
7ISOLDE1.7model fitting
11cryoSPARC4.5.1classification
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 280177
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22169 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: Modeller / Type: in silico model

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