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- EMDB-50448: SSU(head) structure derived from the SSU sample of the mitoriboso... -

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Basic information

Entry
Database: EMDB / ID: EMD-50448
TitleSSU(head) structure derived from the SSU sample of the mitoribosome from T. gondii.
Map dataDeepEMhanced map of the SSU head structure derived from the monosome sample of the mitoribosome from T. gondii.
Sample
  • Complex: SSU head structure sample of the mitoribosome from T. gondii.
    • Protein or peptide: x 20 types
    • RNA: x 8 types
KeywordsComplex / translation / rRNA / RIBOSOME
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
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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRocha REO / Barua S / Boissier F / Nguyen TT / Hashem Y
Funding supportEuropean Union, 1 items
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, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50448.png

Downloads & links

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Map

FileDownload / File: emd_50448.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhanced map of the SSU head structure derived from the monosome sample of the mitoribosome from T. gondii.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 420 pix.
= 632.394 Å		1.51 Å/pix.
x 420 pix.
= 632.394 Å		1.51 Å/pix.
x 420 pix.
= 632.394 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.015722943 - 1.7242327
Average (Standard dev.)0.0003598945 (±0.010079331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 632.394 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50448_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of the SSU head structure derived...

Fileemd_50448_additional_1.map
AnnotationSharpened map of the SSU head structure derived from the monosome sample of the mitoribosome from T. gondii.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the SSU head structure...

Fileemd_50448_half_map_1.map
AnnotationHalf map A of the SSU head structure derived from the monosome sample of the mitoribosome from T. gondii.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the SSU head structure...

Fileemd_50448_half_map_2.map
AnnotationHalf map B of the SSU head structure derived from the monosome sample of the mitoribosome from T. gondii.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SSU head structure sample of the mitoribosome from T. gondii.

EntireName: SSU head structure sample of the mitoribosome from T. gondii.
Components
  • Complex: SSU head structure sample of the mitoribosome from T. gondii.
    • Protein or peptide: Small ribosomal subunit protein mS29,mS29(DAP3)
    • Protein or peptide: Ribosomal protein S9, putative
    • Protein or peptide: uS10m
    • Protein or peptide: Ribosomal protein S14, putative
    • Protein or peptide: mS157
    • Protein or peptide: DNA double-strand break repair rad50 ATPase
    • Protein or peptide: mS149
    • Protein or peptide: ms158
    • Protein or peptide: mS151
    • Protein or peptide: 30S ribosomal protein S5, putative
    • Protein or peptide: mS155
    • Protein or peptide: mS159
    • Protein or peptide: RAP domain-containing protein
    • Protein or peptide: mS161
    • Protein or peptide: mS152
    • Protein or peptide: Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein
    • Protein or peptide: mS141
    • Protein or peptide: AP2 domain transcription factor AP2IX-6
    • Protein or peptide: Acylphosphatase-like domain-containing protein
    • Protein or peptide: mS33/mS27
    • RNA: SSUB-SSU
    • RNA: SSUD
    • RNA: ulr22
    • RNA: RNA9-SSU
    • RNA: RNA5-SSU
    • RNA: ulr23
    • RNA: RNA19-SSU
    • RNA: ulr24

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Supramolecule #1: SSU head structure sample of the mitoribosome from T. gondii.

SupramoleculeName: SSU head structure sample of the mitoribosome from T. gondii.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Toxoplasma gondii (eukaryote) / Organelle: Mitochondria / Location in cell: Cytoplasm

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

MacromoleculeName: Small ribosomal subunit protein mS29,mS29(DAP3) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 57.323969 KDa
SequenceString: VGVEDVGRFR LFDRHRLVEL LPEGLAGELS RDVEMIPSAT SPIGVMLRKA TLELQMQLEL FARVHAKSSA DTRGETPLPR KRKETRKDG ERDAREKKKD EGKDKDGGVG GRGLEEIGSR RSEDEWRERL SELRPFDARL AAVQRGFLLD GHRGVGKSCV L NYLIPWAR ...String:
VGVEDVGRFR LFDRHRLVEL LPEGLAGELS RDVEMIPSAT SPIGVMLRKA TLELQMQLEL FARVHAKSSA DTRGETPLPR KRKETRKDG ERDAREKKKD EGKDKDGGVG GRGLEEIGSR RSEDEWRERL SELRPFDARL AAVQRGFLLD GHRGVGKSCV L NYLIPWAR ENNWLVVYEP LPSRYAREIG DIKRSSAGVY IQSSFSQEFL ERLGRFNRRL LEELPVARRC YGQAALDGVH RL YAERSYH SLLEKALEKD LDEIREQRDE ELKRGSPHSG KDADLLDSQL REEILLARER LALWHTYRRE VSIPSMKSRL PNP ASVWEI AEFGLQNEAF ATQALYEVWE QLKKQTQLNV LIAVDEWNEC FPVSEYVSMR YEGTRFNGHI PAFHLSTPRL LSRF DDAQQ FQRGLKICAT SWRRSNRRDY RPDLLGVRQE EIRTVRNFSP LEFANFVAYY HKKKILHEFP REKLDYFYML SGGNG FQAR RLLASLYGG

UniProtKB: Small ribosomal subunit protein mS29

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Macromolecule #2: Ribosomal protein S9, putative

MacromoleculeName: Ribosomal protein S9, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 17.6374 KDa
SequenceString:
SSDSALISGA IVRAFNPERM KVFMHNGCEW LWQAEGTGTR KRAAAHVIIR RGTGQVRVNN DEDLYVRWPF YYNRMDVLQP FFLTGTAGI YDLFIHVRGG GSSGQAGAVR LAVGRALVSA CPACARLLEE DMVLYEDTRQ RMPKMPGRMK ARKMRTW

UniProtKB: Ribosomal protein S9, putative

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Macromolecule #3: uS10m

MacromoleculeName: uS10m / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 26.630137 KDa
SequenceString: ALSAYSLRSL IVTYNSRNRS SMNATIENLK NALRWTSPSE SSSPSSAPSS APSSAPSSSW SPPWPVPRRV GRRQWRVTYL KSPFKYKYA LRHYVFEDHR YAFAFYDVNS VQEVVSAALG AMAGETCCSC RFSWRFAGRP PVSLPTPPRL VPSSRAASLL S SRSSSEDG ...String:
ALSAYSLRSL IVTYNSRNRS SMNATIENLK NALRWTSPSE SSSPSSAPSS APSSAPSSSW SPPWPVPRRV GRRQWRVTYL KSPFKYKYA LRHYVFEDHR YAFAFYDVNS VQEVVSAALG AMAGETCCSC RFSWRFAGRP PVSLPTPPRL VPSSRAASLL S SRSSSEDG EVSREPVEGG EKTSGVKKAP HLATVLRGHC PTDKEFIRRA LEEEQAVERI RKKLDKKQLQ WFPGKTPWAP

UniProtKB: Uncharacterized protein

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Macromolecule #4: Ribosomal protein S14, putative

MacromoleculeName: Ribosomal protein S14, putative / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 12.011157 KDa
SequenceString:
LNPPPIAFPS FNRRCQKDWL ARRAFAENEV NGRIYKNVYQ NLGFKGPIPI LNKVGQYRIR MRCISGGYSR GIFRFTRMAR MGMLQLARE GWLKKYGYRP GLF

UniProtKB: Ribosomal protein S14, putative

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Macromolecule #5: mS157

MacromoleculeName: mS157 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 18.921652 KDa
SequenceString:
ARRVGGIGRR CFLTLHCSAC SFFFQTSDAI KLILTQQHHI LRKKGETRFL SGASGDAVHL ESVGASNEAQ GNRPSSSSSP SSSGGTRDK GVSRRVVAAA ASSAASKFSL LPLADASLLL KRRGALVLRS LHGDPLVGSR RQRGEFAPQA PTAEMAKMLN K SCVPCPRC KREGRWEEG

UniProtKB: Uncharacterized protein

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Macromolecule #6: DNA double-strand break repair rad50 ATPase

MacromoleculeName: DNA double-strand break repair rad50 ATPase / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 40.243094 KDa
SequenceString: YITSANFSEP VELLSLAEDL HKAEIYTQTT EKLEKQWPAA GGVAKGIQGD QFFDVMAAAV REDLQDQSRP VLVNELTDHE NPYCMKREA LRRLVLHACT RNCLDETLTD TLLDRRADLQ RLRSKARLPP EVLEPLAAFV GITRFSFDRR ARLNQKVTAV Q HALRQISL ...String:
YITSANFSEP VELLSLAEDL HKAEIYTQTT EKLEKQWPAA GGVAKGIQGD QFFDVMAAAV REDLQDQSRP VLVNELTDHE NPYCMKREA LRRLVLHACT RNCLDETLTD TLLDRRADLQ RLRSKARLPP EVLEPLAAFV GITRFSFDRR ARLNQKVTAV Q HALRQISL DGVNTAELAE GQDEPTMDAE KVEAVLSVLP ENFPSDALHP HHPFRNHFGF ESSVPYGVVG SISMGKGRKK IE KELARLR YPTLQRVAHS LPKDLKYRES VAHAIRVLER SRGWDFESKV KAVNALVEVW NRLAPGRTYE KILNHAFPVF RGR GMVKKT RSRAAVFNKG LKYIRSLTTQ KPLHARLQ

UniProtKB: DNA double-strand break repair rad50 ATPase

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Macromolecule #7: mS149

MacromoleculeName: mS149 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 10.301842 KDa
SequenceString:
PAERLHSLFA RADVLAHLLH SRLALPLLYP LNSGGALTNP LNSAASPDSP AALNSIATSR WKREEVMSAL ATVTPLVLAA TSVSRFLKT AHALSYFA

UniProtKB: Uncharacterized protein

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Macromolecule #8: ms158

MacromoleculeName: ms158 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 10.757225 KDa
SequenceString:
PEAPQPPAGL HWSWWELYVK GVNPEYPPRQ RMFAFLTAQG VDVLEMEIRE IEDVTRWLEM SNVYGEKFPR FPYDVTFQDK IEALKEKYP L

UniProtKB: Uncharacterized protein

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Macromolecule #9: mS151

MacromoleculeName: mS151 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 17.023863 KDa
SequenceString:
AFRYRREGQF TKFRVHFDRS GFRPYIDELK WEIMDWHYKR AMGPQMKKTL MSYQEGSEKL QYMHDLIALG TAKAKFPHAT KRFFFVPAL PVTIPYRRSS NPFCLLSANK TGWLQWSPKQ RVPFPQPLGK RKVGGTDPQP PVFPK

UniProtKB: Uncharacterized protein

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Macromolecule #10: 30S ribosomal protein S5, putative

MacromoleculeName: 30S ribosomal protein S5, putative / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 49.936402 KDa
SequenceString: LQELESFVGS ALRTYRLLRP HALPFYKEDS LLSMQSKLNE ATLKHSPLVH DLVELKKRNL SVPSDLLPPD FNALQFSLPV VSARGFLLA LSAAANSVAE DLEFLCRRLS VPNLPHPTHP FRLKLLLDAL FESFKLRKDP HYAHDWAQRN WPRLQAAMPE P LSELSADS ...String:
LQELESFVGS ALRTYRLLRP HALPFYKEDS LLSMQSKLNE ATLKHSPLVH DLVELKKRNL SVPSDLLPPD FNALQFSLPV VSARGFLLA LSAAANSVAE DLEFLCRRLS VPNLPHPTHP FRLKLLLDAL FESFKLRKDP HYAHDWAQRN WPRLQAAMPE P LSELSADS VGLWLKAHLE RVIENQRGRH ADGRGRLLAQ KFPLKSDEED LYSLADDFIF DHEIVDEQFC DERLSQFPID KA GELFRRV ADFFGLTKGP QPAVNDAVVA QFQNLVYTLD EIGLSNWMKM DTREIEEFLP EGDPPSFAAS QQDLDAARLL LKA AARGKA NLLDFEALDP YKLLHGFDFK TVQEELATLP PNPFLTDADI DELFDITTAA VSMNQSEVAP SASLRNFKAK FGRT PLEAL LDSEEKFLTS AGPVDWLKDE DENGEAFVSW RWKRPA

UniProtKB: 30S ribosomal protein S5, putative

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Macromolecule #11: mS155

MacromoleculeName: mS155 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 14.861185 KDa
SequenceString:
EEDDSVYRQF ACMRRVREEP RLRTALESFK VASKNATKTR GRAWSVYEGW PPRSRVRVGD EYSKVGPLQR RAFVFNRVDG TGRRREPTL AFCCGNKPVL LLSEAEFEAL VKKLPWIKHE MAEFKKLL

UniProtKB: Uncharacterized protein

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Macromolecule #12: mS159

MacromoleculeName: mS159 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 9.367294 KDa
SequenceString:
RQAKKQTKLA AKNARKMKES KGLLLEGKKT ALCMNLMQNT GIAWYRSLQV CKHLEMHRRA PVPRVTAGFR EKVTQAVAVV KLG

UniProtKB: Uncharacterized protein

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Macromolecule #13: RAP domain-containing protein

MacromoleculeName: RAP domain-containing protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 66.455188 KDa
SequenceString: FSSLRLSQKD ARGSGYLPAQ RFLSLLKASP EEYRSLLREA TQAKIVDPAF LRVASQRFFA LSDRFYPPEI LDILSDFASF PYSDEALLA AVAGRLEDQL VEPSPKRLAA LLSLSARLGL CHPSIRDPLT KHIEEKMYAF DAALLDSLCR TVGSLLSPRL P LLDGLATQ ...String:
FSSLRLSQKD ARGSGYLPAQ RFLSLLKASP EEYRSLLREA TQAKIVDPAF LRVASQRFFA LSDRFYPPEI LDILSDFASF PYSDEALLA AVAGRLEDQL VEPSPKRLAA LLSLSARLGL CHPSIRDPLT KHIEEKMYAF DAALLDSLCR TVGSLLSPRL P LLDGLATQ AQLLASDLRA GEQSLETGDE VAQRRYIALL FRCLEGLSRQ RYSQSALVDA CVACAEQHGQ AFPLHDTLRA VA AARRLDL AGIEEPLRRS DMADKVNRAT DRGDQLLALL RHLDLLRLRD SQLLQKVSEA VELHSQKAAF LATQLPEALL HLT RLAPAD LRLPVALLSQ PSLLAMAPRL SAAQLQQLLS ASALVLFQHI QRREGGQGGD PLIAREAEAL AKTVERFLDL LKPQ FLSLN LRDRRALKEA ASLFLVEAKG AAKSSAASPQ FALAPKTVDF CCFLEEADVA PPLPLAPSGG VDFQSVGLVE ACSRL VLCA DARFSETRNS ARGASEGDTK KGDSEKTSLP QTAGRDMEAA AKQRALLFVS PRDAFADARR SRGETVSKSS KAKERE ETT TCKLGGVSTD LPVSITPQAA SSLLLTQLAL IRRGILRHEI QTCIPPP

UniProtKB: RAP domain-containing protein

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Macromolecule #14: mS161

MacromoleculeName: mS161 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 3.360138 KDa
SequenceString:
CMNKKNRLAL RKRRRRMGER VSLRYR

UniProtKB: Uncharacterized protein

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Macromolecule #15: mS152

MacromoleculeName: mS152 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 19.762867 KDa
SequenceString:
TRGFRWDLCQ RGRRRWVHIN YPPRNRSTVQ MLDESHEKLV FVCNGYIDRL DPRLLPERLR KRLERNRKAA LTRFDGKLPW GQAVESAIK RIHTPCLAFA QAHSHHLLEA FSMAEVLEIE KLIPEIREAF KASKAKLAEQ EAQDKFTRHV SVDLVDLKED P VSFPFTLK

UniProtKB: Uncharacterized protein

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Macromolecule #16: Small ribosomal subunit protein mS35 mitochondrial conserved doma...

MacromoleculeName: Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 27.990826 KDa
SequenceString: KKKRGKKEKV ILNAEQVATK TRLPPIRLED RITPEPPATV ARNIRSQISR AVAGWKTKRM FTYRNKYRLR RLVGMTHDID SDDEFAQAN ARTRETNAST SKVSSSGCST EKAEGVNGST MGRRNRPSFA GRTFVTPLTK LQHQAALPRS PLHARFDFPH T VHYDVFWG ...String:
KKKRGKKEKV ILNAEQVATK TRLPPIRLED RITPEPPATV ARNIRSQISR AVAGWKTKRM FTYRNKYRLR RLVGMTHDID SDDEFAQAN ARTRETNAST SKVSSSGCST EKAEGVNGST MGRRNRPSFA GRTFVTPLTK LQHQAALPRS PLHARFDFPH T VHYDVFWG PPQVEEEPNK SGCWVSFRVA DLKLSDSQEQ RLLDILGPER YDEQTGVVCL EADVFPQLNH NAAYLGDILQ QL MREVKK

UniProtKB: Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein

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Macromolecule #17: mS141

MacromoleculeName: mS141 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 82.984148 KDa
SequenceString: LLDTGEIVPG AFASVKKVGD FPLLPLSLLL SRLKERRQEL LRDWQVHAVR QAAVREPLAE ATRENDGGAG PRAVEAFARE EERIQRKIK ILELLACGGL EENASSQGAI GDAKRIAFLA HADAVNLLLL LAAEAETLAR PGEREETEGK EGSSAVGEIS K QEERQLWR ...String:
LLDTGEIVPG AFASVKKVGD FPLLPLSLLL SRLKERRQEL LRDWQVHAVR QAAVREPLAE ATRENDGGAG PRAVEAFARE EERIQRKIK ILELLACGGL EENASSQGAI GDAKRIAFLA HADAVNLLLL LAAEAETLAR PGEREETEGK EGSSAVGEIS K QEERQLWR LKCEGNEEKW NLCISRLKEL ALDHEDSFLV FYAMCSTNRF DAVLLPALLE RLEASFFSSQ ALSKPLFHPI FE VWDPPCE SFAALINVLP LSAKAVVVTA DRRSERERRE NEGWLAPPEA PPLVLPNWQT MHPVDMEAWE KKQRRVVRTR HVK AKIIRQ ADGRKLAATM ALHGRQAIHR DAAVSSLVSV AAMCASNSQR ALRGELLPET LNLLAAELLG RSADALSPHL LSLS FLLSQ SSVSLTERLF LHLEAVLRGW LEENGFVEKK QTENVDGESK ELCTETASEK RRKASEEQLR NLPPGLNVFG LVQSS PSSS DALLASGERS ETSKSADTES ALWESRVLAA LLSSFLRVDD YRPSLDFVLL LSDALRNSLR RTAVLSSASE SSAPLA IHE KDVLSLKETG ALLSSFATSG YAVPPSLMAC LVEHFLYDVD LFLTSSPLSP FASSPSSSSS SAEEAEQLSQ SFFCSSR GR ATPGDCATLL HSLASPSPLS SERLAAADKA GEQKTANLEK LRFEAMTQAW RLVAPVLHLL QPPCKLLILN SLQTAHAP P DVSSTAFFQR SLETFLRDNP DVDSSLLGSL FGTQGR

UniProtKB: Uncharacterized protein

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Macromolecule #18: AP2 domain transcription factor AP2IX-6

MacromoleculeName: AP2 domain transcription factor AP2IX-6 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 20.114152 KDa
SequenceString:
RQEFFWPEKA RRTRVPLYQN SRPNLVYDQR FRRFMCMWYA NGVQVFRPFS CRGRRGGRGK EGLPDGLGIG RGSGTWERAR AKAVVLLKQ LQRQGHLDRL AKPDVTRSGV RGVYFDTEEK LWVATWNEHG LRRFKAFPTM EMGFDAAYQA AVAVRRQKLR E NYIFSMQR NR

UniProtKB: AP2 domain transcription factor AP2IX-6

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Macromolecule #19: Acylphosphatase-like domain-containing protein

MacromoleculeName: Acylphosphatase-like domain-containing protein / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 14.236105 KDa
SequenceString:
TAPRVVRDRD ETNFHEMLGK FRFDLQGSFK ENGDMLRDSL LQVGRDLFLV GWVKCRSRFA TGHIQGDVHA LSYMRRYLEK HVDESVSSV RFYEENFGMP LLEYERLSAV NDFRAPGKKQ QH

UniProtKB: Acylphosphatase-like domain-containing protein

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Macromolecule #20: mS33/mS27

MacromoleculeName: mS33/mS27 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 46.515633 KDa
SequenceString: MRRLASPSLR RLQEGQTPHS MRKSAVADAR KKIFGYACGM PGEEQWVRPL QGRQMMKWYW PSKYMLQDVQ MAQYFQMQAM RFAPRPAHV SLTTLSATME QCWKKRDAVR AFFQSIDEKV LRENPTLQDL YGLYRTLCPD DPLRTPVDPA LWRDPGFTWQ H TADQRIVS ...String:
MRRLASPSLR RLQEGQTPHS MRKSAVADAR KKIFGYACGM PGEEQWVRPL QGRQMMKWYW PSKYMLQDVQ MAQYFQMQAM RFAPRPAHV SLTTLSATME QCWKKRDAVR AFFQSIDEKV LRENPTLQDL YGLYRTLCPD DPLRTPVDPA LWRDPGFTWQ H TADQRIVS SSTNREQQGD PSEPAMATRR VAQEQATDKR HISPANINDD VAALLFSRTE QSGAIRNVCA ASPYLHGGKN NR SRDRFHN GAREANSSEE DSLEQPKSLI LDTESRGTAL SRSRTQECLL ALSALAETGL GQSASELIQQ PVVLRVDIGL GDR EPVQDT TAFRKKQEQS RRTLQAALDH DERLARYHGA KHRFFDPLFR RRRLSFLDRF ARERIKGEKA RQLGAQLYVK HPDQ KPVWP

UniProtKB: Uncharacterized protein

+
Macromolecule #21: SSUB-SSU

MacromoleculeName: SSUB-SSU / type: rna / ID: 21 / Number of copies: 1
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 18.433896 KDa
SequenceString:
UAGACUAGCG UUGGAGCACA UUGUUUCAUU CGAUAGUCCA CGCUCAAUCU UACCAUAC

GENBANK: GENBANK: MN077097.1

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Macromolecule #22: SSUD

MacromoleculeName: SSUD / type: rna / ID: 22 / Number of copies: 1
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 18.120838 KDa
SequenceString:
GGAAGCUGGA AGACGGAAUC GUUAUUAAGC GCCAGGUAGU CCUGGACACU GAAUCC

GENBANK: GENBANK: MN077099.1

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Macromolecule #23: ulr22

MacromoleculeName: ulr22 / type: rna / ID: 23 / Number of copies: 1
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 4.547529 KDa
SequenceString:
UUUUUUUUUU UUUUU

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Macromolecule #24: RNA9-SSU

MacromoleculeName: RNA9-SSU / type: rna / ID: 24 / Number of copies: 1
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 21.695828 KDa
SequenceString:
UUCACCUAGC CAACACGAUC CGGUUGUUUG GGAACAAUUC CCUUCUAGAA GGGUAAUCUA UGUGCUAC

GENBANK: GENBANK: MN077095.1

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Macromolecule #25: RNA5-SSU

MacromoleculeName: RNA5-SSU / type: rna / ID: 25 / Number of copies: 1
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 10.621321 KDa
SequenceString:
CGUAGCUGUA GAUGAAUGCU AAUUAUAGAG UAU

+
Macromolecule #26: ulr23

MacromoleculeName: ulr23 / type: rna / ID: 26 / Number of copies: 1
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 3.0167 KDa
SequenceString:
UUUUUUUUUU

+
Macromolecule #27: RNA19-SSU

MacromoleculeName: RNA19-SSU / type: rna / ID: 27 / Number of copies: 1
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 8.653128 KDa
SequenceString:
UAUUGUGUUA GCAUGGUUUC GAGAACA

+
Macromolecule #28: ulr24

MacromoleculeName: ulr24 / type: rna / ID: 28 / Number of copies: 1
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 5.159861 KDa
SequenceString:
UUUUUUUUUU UUUUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting force 5, blotting time 2.5 seconds..

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 90.0 K / Max: 95.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 9524 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 280177
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22169
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 4 / Avg.num./class: 70000 / Software - Name: cryoSPARC (ver. 4.5.1)

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Atomic model buiding 1

Initial modelChain - Source name: Modeller / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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