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- PDB-9g6k: LSU structure derived from the LSU sample of the mitoribosome fro... -

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Basic information

Entry
Database: PDB / ID: 9g6k
TitleLSU structure derived from the LSU sample of the mitoribosome from T. gondii.
Components
  • (AP2 domain transcription factor ...) x 2
  • (Large ribosomal subunit protein ...) x 10
  • (Putative 50S ribosomal protein ...) x 5
  • (Putative ribosomal protein ...) x 2
  • (RAP domain-containing ...) x 8
  • (Ribosomal protein ...) x 4
  • (Transmembrane ...) x 2
  • AMP-dependent synthetase/ligase domain-containing protein
  • BIR protein
  • DUF6832 domain-containing protein
  • FAS1 domain-containing protein
  • HECT-domain (Ubiquitin-transferase) domain-containing protein
  • LSU ribosomal protein L2P, putative
  • LSUA
  • LSUB
  • LSUC
  • LSUD/E
  • LSUF/G
  • Macro domain-containing protein
  • Peptidyl-prolyl cis-trans isomerase
  • Putative 60S ribosomal protein L27
  • RNA1
  • RNA10
  • RNA11
  • RNA13
  • RNA14
  • RNA15
  • RNA16
  • RNA2
  • RNA23t
  • RNA29
  • RNA3
  • RNA31
  • RNA32
  • RNA35
  • RNA36
  • RNA37
  • RNA38
  • RNA6
  • RNA7
  • RRM domain-containing protein
  • Ribosomal L22p/L17e protein
  • Ribosomal l25 family protein
  • SSUF
  • bL19m
  • bL27m
  • bL32m
  • bL35m
  • bL36m
  • mL148
  • mL162
  • mL164
  • mL172
  • mL173
  • mL174
  • mL175
  • mL176
  • mL177
  • mL178
  • mL179
  • mL180
  • mL181
  • mL182
  • mL183
  • mL184
  • mL185
  • mL40
  • mL53
  • uL14m
  • uL1m
  • ulr1
  • ulr2
  • ulr3
  • ulr4
  • ulr5
  • ulr6
  • ulr7,ulr8
  • ulr9
KeywordsRIBOSOME / Complex / translation / rRNA
Function / homology
Function and homology information


regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial translation / cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ubiquitin-protein transferase activity / protein folding ...regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial translation / cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ubiquitin-protein transferase activity / protein folding / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / DNA-binding transcription factor activity / ribonucleoprotein complex / mRNA binding / DNA binding / RNA binding / nucleus / membrane / cytoplasm
Similarity search - Function
HECTD4 / : / : / : / Domain of unknown function (DUF6831) / Domain of unknown function (DUF6832) / Apicomplexa microprotein / Apicomplexa microprotein / RAP domain / RAP domain ...HECTD4 / : / : / : / Domain of unknown function (DUF6831) / Domain of unknown function (DUF6832) / Apicomplexa microprotein / Apicomplexa microprotein / RAP domain / RAP domain / RAP domain profile. / RAP / AP2 domain / AP2/ERF domain / : / FAS1 domain / FAS1 domain superfamily / FAS1/BIgH3 domain profile. / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / ANL, N-terminal domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / RNA-binding domain superfamily / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Prokaryotic membrane lipoprotein lipid attachment site profile. / Ribosomal protein L2, domain 3 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding N-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / KOW (Kyprides, Ouzounis, Woese) motif.
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL24c / Ribosomal protein L11, putative / Uncharacterized protein / Ribosomal protein RPL22 / Large ribosomal subunit protein mL49 ...RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL24c / Ribosomal protein L11, putative / Uncharacterized protein / Ribosomal protein RPL22 / Large ribosomal subunit protein mL49 / Uncharacterized protein / Putative 50S ribosomal protein L33 / Uncharacterized protein / Large ribosomal subunit protein uL24c / Putative 60S ribosomal protein L27 / Uncharacterized protein / Large ribosomal subunit protein uL4m / BIR protein / Putative 50S ribosomal protein L13 / Putative ribosomal protein L28 / Large ribosomal subunit protein uL29m / Uncharacterized protein / AP2 domain transcription factor AP2VIIb-2 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL3m / RAP domain-containing protein / Ribosomal L22p/L17e protein / Transmembrane protein / Large ribosomal subunit protein bL21m / Putative 50S ribosomal protein L16 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / DUF6832 domain-containing protein / Large ribosomal subunit protein mL43 / Uncharacterized protein / Uncharacterized protein / AP2 domain transcription factor AP2IV-1 / Uncharacterized protein / Putative 50S ribosomal protein L17 / Uncharacterized protein / Putative ribosomal protein L20 / Uncharacterized protein / RAP domain-containing protein / Ribosomal l25 family protein / Uncharacterized protein / RAP domain-containing protein / Ribosomal protein L46 / Large ribosomal subunit protein mL54 / RAP domain-containing protein / Large ribosomal subunit protein uL2m / RRM domain-containing protein / FAS1 domain-containing protein / AMP-dependent synthetase/ligase domain-containing protein / Peptidyl-prolyl cis-trans isomerase / RAP domain-containing protein / Uncharacterized protein / Ribosomal protein L9, N-terminal domain-containing protein / RAP domain-containing protein / Macro domain-containing protein / RAP domain-containing protein / Ribosomal protein L15, putative / HECT-domain (Ubiquitin-transferase) domain-containing protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsRocha, R.E.O. / Barua, S. / Boissier, F. / Nguyen, T.T. / Hashem, Y.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101088541European Union
Citation
Journal: 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.
#1: Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
#2: Journal: Protein Sci / Year: 2021
Title: UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Authors: Eric F Pettersen / Thomas D Goddard / Conrad C Huang / Elaine C Meng / Gregory S Couch / Tristan I Croll / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) ...UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Authors: Tristan Ian Croll /
Abstract: This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density ...This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
History
DepositionJul 18, 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
L0: RRM domain-containing protein
L1: Large ribosomal subunit protein mL54
L2: mL162
L3: Ribosomal l25 family protein
L4: RAP domain-containing protein
L5: mL183
L6: uL1m
L7: uL14m
L8: Putative 50S ribosomal protein L17
L9: DUF6832 domain-containing protein
LA: Putative 50S ribosomal protein L13
LB: Putative ribosomal protein L20
LC: Macro domain-containing protein
LD: Ribosomal protein L46
LE: FAS1 domain-containing protein
LF: bL36m
LG: Ribosomal protein RPL22
LH: Ribosomal protein L9, N-terminal domain-containing protein
LI: Putative 60S ribosomal protein L27
LJ: RAP domain-containing protein
LK: BIR protein
LL: AMP-dependent synthetase/ligase domain-containing protein
LM: Large ribosomal subunit protein uL11m
LN: bL35m
LO: LSU ribosomal protein L2P, putative
LP: Peptidyl-prolyl cis-trans isomerase
LQ: mL175
LR: mL172
LS: Large ribosomal subunit protein uL24c
LT: Putative 50S ribosomal protein L33
LU: Large ribosomal subunit protein mL49
LV: mL148
LW: Putative 50S ribosomal protein L3
LX: mL176
LY: Ribosomal L22p/L17e protein
LZ: mL174
La: Large ribosomal subunit protein uL23m
Lb: RAP domain-containing protein
Lc: RAP domain-containing protein
Ld: RAP domain-containing protein
Le: RAP domain-containing protein
Lf: HECT-domain (Ubiquitin-transferase) domain-containing protein
Lg: Large ribosomal subunit protein uL29m
Lh: Large ribosomal subunit protein uL4m
Li: RAP domain-containing protein
Lj: mL177
Lk: AP2 domain transcription factor AP2VIIb-2
Ll: Large ribosomal subunit protein mL43
Lm: Large ribosomal subunit protein uL24c
Ln: mL185
Lo: Transmembrane protein
Lp: bL19m
Lq: RAP domain-containing protein
Lr: Putative ribosomal protein L28
Ls: Ribosomal protein L15, putative
Lt: mL40
Lu: mL164
Lv: mL180
Lw: Putative 50S ribosomal protein L16
Lx: mL173
Ly: Large ribosomal subunit protein bL21m
Lz: mL182
UA: mL178
UB: bL27m
UC: mL179
UD: Transmembrane protein
UE: mL53
UF: bL32m
UG: AP2 domain transcription factor AP2IV-1
UH: mL181
UI: mL184
l0: RNA23t
l1: RNA29
l2: LSUB
l3: RNA6
l4: RNA1
l5: RNA31
l6: RNA14
l7: RNA11
l8: RNA36
l9: RNA3
lA: RNA2
lB: RNA38
lC: RNA35
lD: RNA32
lE: RNA15
lF: RNA10
lG: LSUC
lH: RNA16
lI: RNA13
lJ: LSUD/E
lK: SSUF
lL: RNA7
lM: LSUF/G
lN: RNA37
lO: LSUA
lP: ulr1
lQ: ulr2
lR: ulr3
lS: ulr4
lT: ulr5
lU: ulr6
lV: ulr7,ulr8
lW: ulr5
lX: ulr9
lY: ulr7,ulr8


Theoretical massNumber of molelcules
Total (without water)2,690,377106
Polymers2,690,377106
Non-polymers00
Water00
1


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

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Components

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Protein , 35 types, 35 molecules L0L2L3L6L7L9LCLELFLILKLLLNLOLPLQLRLVLXLYLZLfLjLnLpLtLuLvLxLz...

#1: Protein RRM domain-containing protein


Mass: 47857.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F7E5
#3: Protein mL162


Mass: 30027.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A0F7V439
#4: Protein Ribosomal l25 family protein


Mass: 37394.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8ER88
#7: Protein uL1m


Mass: 6736.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#8: Protein uL14m


Mass: 12981.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#10: Protein DUF6832 domain-containing protein


Mass: 55084.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KC93
#13: Protein Macro domain-containing protein


Mass: 57139.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GAV7
#15: Protein FAS1 domain-containing protein


Mass: 37960.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F814
#16: Protein bL36m


Mass: 10376.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KFA2
#19: Protein Putative 60S ribosomal protein L27


Mass: 8731.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JYF7
#21: Protein BIR protein


Mass: 26967.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K0B0
#22: Protein AMP-dependent synthetase/ligase domain-containing protein


Mass: 92873.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F8W6
#24: Protein bL35m


Mass: 13974.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KEG8
#25: Protein LSU ribosomal protein L2P, putative


Mass: 37607.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F793
#26: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 26422.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8FB56, peptidylprolyl isomerase
#27: Protein mL175


Mass: 8480.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: Q1JTA3
#28: Protein mL172


Mass: 15186.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KA70
#32: Protein mL148


Mass: 96130.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8EU00
#34: Protein mL176


Mass: 11108.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K9K6
#35: Protein Ribosomal L22p/L17e protein


Mass: 41242.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K2Q7
#36: Protein mL174


Mass: 22605.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YYR6
#42: Protein HECT-domain (Ubiquitin-transferase) domain-containing protein


Mass: 25178.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GMU2
#46: Protein mL177


Mass: 13903.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JV70
#50: Protein mL185


Mass: 6289.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8G210
#52: Protein bL19m


Mass: 43663.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#56: Protein mL40


Mass: 27113.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KCG7
#57: Protein mL164


Mass: 26163.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#58: Protein mL180


Mass: 13209.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZI4
#60: Protein mL173


Mass: 11371.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KAH2
#62: Protein mL182


Mass: 14083.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#63: Protein mL178


Mass: 10027.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KDX2
#64: Protein bL27m


Mass: 20579.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K1X2
#65: Protein mL179


Mass: 12288.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#67: Protein mL53


Mass: 13313.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JX69
#68: Protein bL32m


Mass: 9466.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K9L3

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Large ribosomal subunit protein ... , 10 types, 10 molecules L1LMLSLULaLgLhLlLmLy

#2: Protein Large ribosomal subunit protein mL54


Mass: 10873.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F6A8
#23: Protein Large ribosomal subunit protein uL11m


Mass: 19700.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YTN1
#29: Protein Large ribosomal subunit protein uL24c


Mass: 25840.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YMH9
#31: Protein Large ribosomal subunit protein mL49


Mass: 8876.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JUD4
#37: Protein Large ribosomal subunit protein uL23m


Mass: 25045.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K299
#43: Protein Large ribosomal subunit protein uL29m


Mass: 25977.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K1F8
#44: Protein Large ribosomal subunit protein uL4m


Mass: 54296.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZZ1
#48: Protein Large ribosomal subunit protein mL43


Mass: 22268.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KC95
#49: Protein Large ribosomal subunit protein uL24c


Mass: 22014.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JXG2
#61: Protein Large ribosomal subunit protein bL21m


Mass: 47176.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K7U7

+
RAP domain-containing ... , 8 types, 8 molecules L4LJLbLcLdLeLiLq

#5: Protein RAP domain-containing protein


Mass: 49298.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8G8G0
#20: Protein RAP domain-containing protein


Mass: 51732.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K2J1
#38: Protein RAP domain-containing protein


Mass: 83547.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F6E9
#39: Protein RAP domain-containing protein


Mass: 58330.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8EW79
#40: Protein RAP domain-containing protein


Mass: 49907.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8EW79
#41: Protein RAP domain-containing protein


Mass: 43435.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GIP4
#45: Protein RAP domain-containing protein


Mass: 67893.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8FC14
#53: Protein RAP domain-containing protein


Mass: 85917.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8EQ41

+
Protein/peptide , 3 types, 3 molecules L5UHUI

#6: Protein/peptide mL183


Mass: 3787.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#70: Protein/peptide mL181


Mass: 5741.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#71: Protein/peptide mL184


Mass: 4226.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A0F7V869

+
Putative 50S ribosomal protein ... , 5 types, 5 molecules L8LALTLWLw

#9: Protein Putative 50S ribosomal protein L17


Mass: 29244.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KEY9
#11: Protein Putative 50S ribosomal protein L13


Mass: 24255.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K0U2
#30: Protein Putative 50S ribosomal protein L33


Mass: 14149.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JWI3
#33: Protein Putative 50S ribosomal protein L3


Mass: 34639.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K2F9
#59: Protein Putative 50S ribosomal protein L16


Mass: 20393.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K7Z7

+
Putative ribosomal protein ... , 2 types, 2 molecules LBLr

#12: Protein Putative ribosomal protein L20


Mass: 14651.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PY19
#54: Protein Putative ribosomal protein L28


Mass: 33213.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K129

+
Ribosomal protein ... , 4 types, 4 molecules LDLGLHLs

#14: Protein Ribosomal protein L46


Mass: 32456.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8EWD8
#17: Protein Ribosomal protein RPL22


Mass: 17693.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JUA9
#18: Protein Ribosomal protein L9, N-terminal domain-containing protein


Mass: 9818.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8G4D4
#55: Protein Ribosomal protein L15, putative


Mass: 36395.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GIU7

+
AP2 domain transcription factor ... , 2 types, 2 molecules LkUG

#47: Protein AP2 domain transcription factor AP2VIIb-2


Mass: 21280.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K291
#69: Protein AP2 domain transcription factor AP2IV-1


Mass: 19040.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KEE5

+
Transmembrane ... , 2 types, 2 molecules LoUD

#51: Protein Transmembrane protein


Mass: 31526.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KAS3
#66: Protein/peptide Transmembrane protein


Mass: 4380.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K730

+
RNA chain , 33 types, 35 molecules l0l1l2l3l4l5l6l7l8l9lAlBlClDlElFlGlHlIlJlKlLlMlNlOlPlQlRlSlT...

#72: RNA chain RNA23t


Mass: 14103.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#73: RNA chain RNA29


Mass: 16107.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#74: RNA chain LSUB


Mass: 9946.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#75: RNA chain RNA6


Mass: 18903.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#76: RNA chain RNA1


Mass: 30072.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#77: RNA chain RNA31


Mass: 11474.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#78: RNA chain RNA14


Mass: 16141.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#79: RNA chain RNA11


Mass: 22303.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#80: RNA chain RNA36


Mass: 10631.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#81: RNA chain RNA3


Mass: 29090.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#82: RNA chain RNA2


Mass: 20904.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#83: RNA chain RNA38


Mass: 14798.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#84: RNA chain RNA35


Mass: 8744.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#85: RNA chain RNA32


Mass: 5058.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#86: RNA chain RNA15


Mass: 9490.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#87: RNA chain RNA10


Mass: 28356.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#88: RNA chain LSUC


Mass: 8406.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#89: RNA chain RNA16


Mass: 8614.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#90: RNA chain RNA13


Mass: 15628.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#91: RNA chain LSUD/E


Mass: 89620.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#92: RNA chain SSUF


Mass: 12351.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#93: RNA chain RNA7


Mass: 29367.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#94: RNA chain LSUF/G


Mass: 62298.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#95: RNA chain RNA37


Mass: 19888.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#96: RNA chain LSUA


Mass: 57982.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#97: RNA chain ulr1


Mass: 8833.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#98: RNA chain ulr2


Mass: 11283.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#99: RNA chain ulr3


Mass: 8527.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#100: RNA chain ulr4


Mass: 2098.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#101: RNA chain ulr5


Mass: 4241.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#102: RNA chain ulr6


Mass: 4547.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#103: RNA chain ulr7,ulr8


Mass: 3016.700 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#104: RNA chain ulr9


Mass: 17712.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

+
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

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Sample preparation

ComponentName: LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Toxoplasma gondii (eukaryote)
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
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blotting force 5, blotting time 2.5 seconds.

-
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
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: 2.89 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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