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- PDB-6xyw: Structure of the plant mitochondrial ribosome -

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Basic information

Entry
Database: PDB / ID: 6xyw
TitleStructure of the plant mitochondrial ribosome
Components
  • (30S ribosomal protein ...) x 3
  • (40S ribosomal protein ...) x 3
  • (50S ribosomal protein ...) x 8
  • (60S ribosomal protein ...) x 3
  • (Mitochondrial ...) x 2
  • (Pentatricopeptide repeat-containing protein ...) x 3
  • (Ribosomal protein ...) x 11
  • (Uncharacterized ...) x 2
  • (rPPR*) x 4
  • 28S ribosomal S34 protein
  • 3-hydroxyisobutyryl-CoA hydrolase-like protein 2, mitochondrial
  • 37S ribosomal protein S27
  • 39S ribosomal protein
  • AT1G52370 protein
  • AT3G18240 protein
  • AT4g31460/F3L17_30
  • AT5g49210/K21P3_8
  • Adenylyl cyclase
  • At1g01640
  • At1g07830/F24B9_7
  • At1g14620/T5E21_15
  • At1g15810/F7H2_23
  • At1g24240/F3I6_17
  • At1g26740/T24P13_11
  • At1g64880
  • At1g73940/F2P9_19
  • At2g34520
  • At3g06320
  • At3g51010
  • At4g05400
  • At4g22000
  • At4g35490
  • At4g39880
  • At5g09770
  • At5g26800
  • At5g27820
  • At5g40080
  • At5g55140
  • CX9C domain-containing protein
  • Expressed protein
  • F10K1.8 protein
  • Gb|AAC32909.1
  • Nucleic acid-binding, OB-fold-like protein
  • Probable ribosomal protein S11, mitochondrial
  • Putative ribosomal protein L6
  • RNA (118-MER)
  • RNA (1743-MER)
  • RNA (2842-MER)
  • Ribosomal protein
  • Small ribosomal subunit protein S13, mitochondrial
  • Translation elongation factor EF1B/ribosomal protein S6 family protein
  • UNK-1
  • UNK-2
  • UNK-3
  • UNK-4
  • UNK-5
  • UNK-6
  • mS31/mS46
  • mS38
KeywordsRIBOSOME / Mitochondria / Plant
Function / homology
Function and homology information


embryo sac central cell differentiation / endosperm cellularization / gametophyte development / pollen tube development / endosperm development / polar nucleus fusion / regulation of starch biosynthetic process / pollen germination / double fertilization forming a zygote and endosperm / 3-hydroxyisobutyryl-CoA hydrolase activity ...embryo sac central cell differentiation / endosperm cellularization / gametophyte development / pollen tube development / endosperm development / polar nucleus fusion / regulation of starch biosynthetic process / pollen germination / double fertilization forming a zygote and endosperm / 3-hydroxyisobutyryl-CoA hydrolase activity / embryo sac development / nucleus localization / pollen development / karyogamy / regulation of programmed cell death / embryo development ending in seed dormancy / cell communication / Hydrolases; Acting on ester bonds; Thioester hydrolases / vacuole organization / plant-type vacuole / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial membrane organization / mitochondrial translation / plastid / translation elongation factor activity / aminopeptidase activity / cytosolic ribosome / response to cold / chloroplast / trans-Golgi network / regulation of translation / large ribosomal subunit / ribosomal small subunit biogenesis / regulation of gene expression / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / transcription cis-regulatory region binding / endosome / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / copper ion binding / ribonucleoprotein complex / mRNA binding / Golgi apparatus / mitochondrion / RNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitochondrial ribosomal protein S7, plants / Ribosomal protein S3, mitochondrial, plant / : / IMS import disulfide relay-system, CHCH-CHCH-like Cx9C / CHCH-CHCH-like Cx9C, IMS import disulfide relay-system, / : / : / 30S ribosomal protein S31, plant / Ribosomal protein S31e / : ...Mitochondrial ribosomal protein S7, plants / Ribosomal protein S3, mitochondrial, plant / : / IMS import disulfide relay-system, CHCH-CHCH-like Cx9C / CHCH-CHCH-like Cx9C, IMS import disulfide relay-system, / : / : / 30S ribosomal protein S31, plant / Ribosomal protein S31e / : / PPR repeat / Mitochondrial ribosomal protein L31 / Ribosomal protein MRP10, mitochondrial / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Small ribosomal subunit protein mS41 SAM domain / PPR repeat family / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / IGR protein motif / IGR / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S34 / Mitochondrial 28S ribosomal protein S34 / : / Pentatricopeptide repeat domain / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Pentatricopeptide (PPR) repeat profile. / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / 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) / 30S ribosomal protein / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ClpP/crotonase-like domain superfamily / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / 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 / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / RNA recognition motif / RNA recognition motif / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein S19, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L36
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein mL43 / Ribosomal protein S21 family protein / Large ribosomal subunit protein mL101 (rPPR4) / At1g24240/F3I6_17 / At4g22000 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein mL43 / Ribosomal protein S21 family protein / Large ribosomal subunit protein mL101 (rPPR4) / At1g24240/F3I6_17 / At4g22000 / Small ribosomal subunit protein mS80 (rPPR6) / Small ribosomal subunit protein uS19m / Large ribosomal subunit protein uL5m / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS7m / Large ribosomal subunit protein uL2mz, N-terminal part / Ribosomal protein L31 / IMS import disulfide relay-system CHCH-CHCH-like Cx9C domain-containing protein / Adenylyl cyclase / Small ribosomal subunit protein uS4m / Large ribosomal subunit protein uL22c / At1g64880 / At5g26800 / At1g01640 / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein uS9m / At1g14620/T5E21_15 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL21m / Ribosomal protein L35 / 50S ribosomal protein L20 / At5g09770 / At5g27820 / Small ribosomal subunit protein mS47 / Large ribosomal subunit protein uL4m / Small ribosomal subunit protein uS11m / Large ribosomal subunit protein uL2my, C-terminal part / Ribosomal protein / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein uL14mz / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein bL32m / AT5g49210/K21P3_8 / Uncharacterized protein At1g27435/F17L21.30 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL16m / Small ribosomal subunit protein uS3m / At1g73940/F2P9_19 / Small ribosomal subunit protein uS13m / 28S ribosomal S34 protein / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain-containing protein / Ribosomal protein L18e/L15 superfamily protein / Small ribosomal subunit protein mL104 (rPPR9) / Small ribosomal subunit protein uS2m / 50S ribosomal protein L10 / AT3g18240 / Small ribosomal subunit protein bS18c / Small ribosomal subunit protein uS15c / Large ribosomal subunit protein uL3m / Translation elongation factor EF1B/ribosomal protein S6 family protein / 50S ribosomal protein L24 / Small ribosomal subunit protein bS16m/bS16c / At5g40080 / Small ribosomal subunit protein mS75 / Large ribosomal subunit protein bL9c / Small ribosomal subunit protein uS8my / At4g05400 / At3g51010 / Small ribosomal subunit protein bTHXm / Large ribosomal subunit protein uL23m / Small ribosomal subunit protein uS14m / 50S ribosomal protein L33, chloroplastic / AT4g31460/F3L17_30 / At4g35490 / Small ribosomal subunit protein uS17c / Putative ribosomal protein L6 / 50S ribosomal protein L27
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsSoufari, H. / Waltz, F. / Bochler, A. / Giege, P. / Hashem, Y.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyMITRA, ANR-16-CE11-0024-02 France
CitationJournal: Nat Plants / Year: 2020
Title: Cryo-EM structure of the RNA-rich plant mitochondrial ribosome.
Authors: Florent Waltz / Heddy Soufari / Anthony Bochler / Philippe Giegé / Yaser Hashem /
Abstract: The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs. These organelles have a bacterial origin and were acquired during an early endosymbiosis event. ...The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs. These organelles have a bacterial origin and were acquired during an early endosymbiosis event. Mitochondria possess specialized gene expression systems composed of various molecular machines, including the mitochondrial ribosomes (mitoribosomes). Mitoribosomes are in charge of translating the few essential mRNAs still encoded by mitochondrial genomes. While chloroplast ribosomes strongly resemble those of bacteria, mitoribosomes have diverged significantly during evolution and present strikingly different structures across eukaryotic species. In contrast to animals and trypanosomatids, plant mitoribosomes have unusually expanded ribosomal RNAs and have conserved the short 5S rRNA, which is usually missing in mitoribosomes. We have previously characterized the composition of the plant mitoribosome, revealing a dozen plant-specific proteins in addition to the common conserved mitoribosomal proteins. In spite of the tremendous recent advances in the field, plant mitoribosomes remained elusive to high-resolution structural investigations and the plant-specific ribosomal features of unknown structures. Here, we present a cryo-electron microscopy study of the plant 78S mitoribosome from cauliflower at near-atomic resolution. We show that most of the plant-specific ribosomal proteins are pentatricopeptide repeat proteins (PPRs) that deeply interact with the plant-specific rRNA expansion segments. These additional rRNA segments and proteins reshape the overall structure of the plant mitochondrial ribosome, and we discuss their involvement in the membrane association and mRNA recruitment prior to translation initiation. Finally, our structure unveils an rRNA-constructive phase of mitoribosome evolution across eukaryotes.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
Aa: 60S ribosomal protein L2, mitochondrial
Ab: Expressed protein
Ac: 50S ribosomal protein L3-2, mitochondrial
AD: Ribosomal protein L35
Ad: 50S ribosomal protein L4
Ae: 60S ribosomal protein L5, mitochondrial
Af: Putative ribosomal protein L6
Ag: Ribosomal protein L9/RNase H1
Ai: At4g35490
Aj: At1g01640
Ak: 50S ribosomal protein HLP, mitochondrial
Al: Ribosomal protein L18e/L15 superfamily protein
Am: 60S ribosomal protein L16, mitochondrial
An: At5g09770
Ao: At5g27820
Ap: At1g24240/F3I6_17
Aq: 50S ribosomal protein L20
Ar: 50S ribosomal protein L21, mitochondrial
As: AT1G52370 protein
At: At4g39880
Au: 50S ribosomal protein L24
Av: Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain-containing protein
Aw: 50S ribosomal protein L27
Ax: AT4g31460/F3L17_30
Ay: At1g07830/F24B9_7
AA: Ribosomal protein L31
AB: At1g26740/T24P13_11
AC: At3g06320
AE: Ribosomal protein
AF: At4g05400
AG: At5g40080
AH: Mitochondrial ribosomal protein L51/S25/CI-B8 family protein
AI: At1g14620/T5E21_15
AJ: 39S ribosomal protein
AK: At4g22000
AL: Uncharacterized protein At1g27435/F17L21.30
AM: At1g73940/F2P9_19
AN: At3g51010
AO: Pentatricopeptide repeat-containing protein At1g60770
AP: rPPR*
AQ: Pentatricopeptide repeat-containing protein PNM1, mitochondrial
AR: UNK-6
1: RNA (2842-MER)
3: RNA (118-MER)
Bb: Ribosomal protein S3, mitochondrial
Bf: Ribosomal protein S7, mitochondrial
Bh: 30S ribosomal protein S9, mitochondrial
Bi: 40S ribosomal protein S10, mitochondrial
Bl: Small ribosomal subunit protein S13, mitochondrial
Bm: At2g34520
Br: 40S ribosomal protein S19, mitochondrial
Bw: Mitochondrial 28S ribosomal protein S29-like protein
Bx: 37S ribosomal protein S27
Bz: AT3G18240 protein
BA: CX9C domain-containing protein
Bt: 30S ribosomal protein S31, mitochondrial
BG: Pentatricopeptide repeat-containing protein At3g02650, mitochondrial
BP: UNK-5
BF: mS31/mS46
Ba: Ribosomal protein S2, mitochondrial
Bc: Ribosomal protein S4, mitochondrial
Bd: At1g64880
Be: Translation elongation factor EF1B/ribosomal protein S6 family protein
Bg: 40S ribosomal protein S15a-5
Bj: Probable ribosomal protein S11, mitochondrial
Bn: At1g15810/F7H2_23
Bo: 30S ribosomal protein S16-2, chloroplastic/mitochondrial
Bp: Nucleic acid-binding, OB-fold-like protein
Bq: F10K1.8 protein
Bs: Ribosomal protein S21 family protein
Bu: Uncharacterized protein
Bv: AT5g49210/K21P3_8
By: 28S ribosomal S34 protein
BB: mS38
BC: At5g26800
BD: Gb|AAC32909.1
BE: 3-hydroxyisobutyryl-CoA hydrolase-like protein 2, mitochondrial
BI: rPPR*
BJ: rPPR*
BH: Adenylyl cyclase
BN: UNK-3
BM: UNK-2
BO: UNK-4
BL: UNK-1
2: RNA (1743-MER)
Az: At5g55140
Ah: 50S ribosomal protein L10
BK: rPPR*
Bk: Ribosomal protein S12, mitochondrial


Theoretical massNumber of molelcules
Total (without water)3,559,85089
Polymers3,559,85089
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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60S ribosomal protein ... , 3 types, 3 molecules AaAeAm

#1: Protein 60S ribosomal protein L2, mitochondrial


Mass: 37982.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P93311
#6: Protein 60S ribosomal protein L5, mitochondrial


Mass: 21258.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P42793
#13: Protein 60S ribosomal protein L16, mitochondrial


Mass: 20132.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q95747

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Protein , 49 types, 49 molecules AbAfAiAjAnAoApAsAtAxAyABACAEAFAGAIAJAKAMANAPBlBmBxBzBABPBFBd...

#2: Protein Expressed protein / Ribosomal protein L2 family


Mass: 22884.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VZU4
#7: Protein Putative ribosomal protein L6 / Ribosomal protein L6 family protein


Mass: 11612.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZPX2
#9: Protein At4g35490 / Mitochondrial ribosomal protein L11 / Ribosomal protein L11 homolog / Ribosomal protein L11-like protein


Mass: 16910.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SVW7
#10: Protein At1g01640 / Ribosomal protein L13 family protein


Mass: 23428.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q7XA68
#14: Protein At5g09770 / Ribosomal protein L17 family protein / Ribsomal protein-like


Mass: 18482.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LD39
#15: Protein At5g27820 / Ribosomal L18p/L5e family protein


Mass: 12762.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LDK5
#16: Protein At1g24240/F3I6_17 / F3I6.17 protein / Ribosomal protein L19 family protein


Mass: 25113.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O48691
#19: Protein AT1G52370 protein / At1g52370 / Chloroplast 50S ribosomal protein L22 / Putative chloroplast 50S ribosomal protein L22 ...At1g52370 / Chloroplast 50S ribosomal protein L22 / Putative chloroplast 50S ribosomal protein L22 / Ribosomal protein L22p/L17e family protein


Mass: 30211.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q56W16
#20: Protein At4g39880 / Ribosomal protein L23/L15e family protein


Mass: 19894.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SMR5
#24: Protein AT4g31460/F3L17_30 / Ribosomal L28 family


Mass: 24112.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SV23
#25: Protein At1g07830/F24B9_7 / Ribosomal protein L29 family protein


Mass: 16913.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94JQ7
#27: Protein At1g26740/T24P13_11 / Ribosomal L32p protein family


Mass: 14823.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q944L5
#28: Protein At3g06320 / At5g18790 / Putative 50S ribosomal protein L33 / Ribosomal protein L33 family protein / Ribosomal ...At5g18790 / Putative 50S ribosomal protein L33 / Ribosomal protein L33 family protein / Ribosomal protein L33-like


Mass: 6975.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SQT5
#29: Protein Ribosomal protein


Mass: 11452.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8W464
#30: Protein At4g05400 / Copper ion binding protein


Mass: 27677.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M0V5
#31: Protein At5g40080 / Mitochondrial ribosomal protein L27


Mass: 10478.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LUJ9
#33: Protein At1g14620/T5E21_15 / Decoy


Mass: 27178.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8L7U3
#34: Protein 39S ribosomal protein


Mass: 14456.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q940G3
#35: Protein At4g22000 / Tyrosine sulfotransferase-like protein


Mass: 15492.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O65448
#37: Protein At1g73940/F2P9_19 / Tumor necrosis factor receptor family protein


Mass: 17112.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C9B5
#38: Protein At3g51010 / Protein translocase subunit


Mass: 21574.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SD44
#40: Protein rPPR*


Mass: 47569.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#49: Protein Small ribosomal subunit protein S13, mitochondrial / mS13


Mass: 17311.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9CA19
#50: Protein At2g34520 / Mitochondrial ribosomal protein S14 / Ribosomal protein S14


Mass: 18778.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SMX4
#53: Protein 37S ribosomal protein S27


Mass: 11558.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8GXH5
#54: Protein AT3G18240 protein / AT3g18240 / Ribosomal protein S24/S35


Mass: 48125.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LJQ6
#55: Protein CX9C domain-containing protein


Mass: 10532.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q1G3Z3
#58: Protein UNK-5


Mass: 6486.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#59: Protein mS31/mS46


Mass: 8760.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#62: Protein At1g64880 / Ribosomal protein S5 family protein


Mass: 60341.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q6GKU7
#63: Protein Translation elongation factor EF1B/ribosomal protein S6 family protein


Mass: 15991.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LSA1
#65: Protein Probable ribosomal protein S11, mitochondrial / S11mt / Protein NUCLEAR FUSION DEFECTIVE 3 / mitochondrial


Mass: 33977.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VZT8
#66: Protein At1g15810/F7H2_23 / F7H2.15 protein / S15/NS1 / RNA-binding protein


Mass: 47401.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LMQ3
#68: Protein Nucleic acid-binding, OB-fold-like protein / Putative 40S ribosomal protein S17 / Putative ribosomal protein


Mass: 12582.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9XIA6
#69: Protein F10K1.8 protein / Ribosomal protein S18


Mass: 29657.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LML3
#72: Protein AT5g49210/K21P3_8 / Stress response NST1-like protein


Mass: 23553.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q945P2
#73: Protein 28S ribosomal S34 protein


Mass: 15793.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FHC3
#74: Protein mS38


Mass: 15934.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#75: Protein At5g26800 / Xaa-pro aminopeptidase P


Mass: 12624.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q6IDB8
#76: Protein Gb|AAC32909.1 / Ribosomal protein L20


Mass: 48396.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LVA9
#77: Protein 3-hydroxyisobutyryl-CoA hydrolase-like protein 2, mitochondrial


Mass: 45548.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q8RXN4, Hydrolases; Acting on ester bonds; Thioester hydrolases
#78: Protein rPPR*


Mass: 18924.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#79: Protein rPPR*


Mass: 24824.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#80: Protein Adenylyl cyclase / At4g15640


Mass: 43971.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q1JPP0
#81: Protein UNK-3


Mass: 4922.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#82: Protein UNK-2


Mass: 5633.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#84: Protein UNK-1


Mass: 4566.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#86: Protein At5g55140 / Ribosomal protein L30 family protein


Mass: 12381.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8L908
#88: Protein rPPR*


Mass: 22478.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

+
50S ribosomal protein ... , 8 types, 8 molecules AcAdAkAqArAuAwAh

#3: Protein 50S ribosomal protein L3-2, mitochondrial


Mass: 35456.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LRN8
#5: Protein 50S ribosomal protein L4 / Ribosomal protein L4/L1 family


Mass: 33315.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VY61
#11: Protein 50S ribosomal protein HLP, mitochondrial / Protein HUELLENLOS PARALOG


Mass: 18601.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q93Z17
#17: Protein 50S ribosomal protein L20


Mass: 14754.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LCN1
#18: Protein 50S ribosomal protein L21, mitochondrial / Protein NUCLEAR FUSION DEFECTIVE 1


Mass: 30955.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8L9A0
#21: Protein 50S ribosomal protein L24 / At5g23535 / KOW domain-containing protein


Mass: 17531.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LT09
#23: Protein 50S ribosomal protein L27 / At2g16930 / Putative 50S ribosomal protein L27 / Ribosomal protein L27 family protein


Mass: 16709.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZVX0
#87: Protein 50S ribosomal protein L10 / 50S ribosomal protein L10 / putative / putative / 89815-90330 / At3g12370 / Ribosomal protein L10 ...50S ribosomal protein L10 / putative / putative / 89815-90330 / At3g12370 / Ribosomal protein L10 family protein


Mass: 19125.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LHH1

+
Ribosomal protein ... , 11 types, 11 molecules ADAgAlAvAABbBfBaBcBsBk

#4: Protein Ribosomal protein L35


Mass: 20109.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LAA7
#8: Protein Ribosomal protein L9/RNase H1 / Similarity to ribosomal protein L9


Mass: 25398.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LVU5
#12: Protein Ribosomal protein L18e/L15 superfamily protein


Mass: 31262.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FLF3
#22: Protein Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain-containing protein


Mass: 27376.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FKZ4
#26: Protein Ribosomal protein L31


Mass: 8972.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q1G3G5
#45: Protein Ribosomal protein S3, mitochondrial


Mass: 64998.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q95749
#46: Protein Ribosomal protein S7, mitochondrial


Mass: 17235.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P92557
#60: Protein Ribosomal protein S2, mitochondrial


Mass: 24808.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9GCB9
#61: Protein Ribosomal protein S4, mitochondrial


Mass: 43477.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q31708
#70: Protein Ribosomal protein S21 family protein


Mass: 11673.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4JCI2
#89: Protein Ribosomal protein S12, mitochondrial


Mass: 14283.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P92532

+
Mitochondrial ... , 2 types, 2 molecules AHBw

#32: Protein Mitochondrial ribosomal protein L51/S25/CI-B8 family protein


Mass: 16667.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4J9E4
#52: Protein Mitochondrial 28S ribosomal protein S29-like protein


Mass: 53863.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8W4K2

+
Uncharacterized ... , 2 types, 2 molecules ALBu

#36: Protein Uncharacterized protein At1g27435/F17L21.30


Mass: 8780.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94F28
#71: Protein Uncharacterized protein


Mass: 22084.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4HPB7

+
Pentatricopeptide repeat-containing protein ... , 3 types, 3 molecules AOAQBG

#39: Protein Pentatricopeptide repeat-containing protein At1g60770


Mass: 55981.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O22714
#41: Protein Pentatricopeptide repeat-containing protein PNM1, mitochondrial / PPR PROTEIN LOCALIZED TO THE NUCLEUS AND MITOCHONDRIA 1


Mass: 59234.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FME4
#57: Protein Pentatricopeptide repeat-containing protein At3g02650, mitochondrial


Mass: 63912.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P0C896

+
Protein/peptide , 2 types, 2 molecules ARBO

#42: Protein/peptide UNK-6


Mass: 2079.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#83: Protein/peptide UNK-4


Mass: 2150.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

+
RNA chain , 3 types, 3 molecules 132

#43: RNA chain RNA (2842-MER)


Mass: 918957.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#44: RNA chain RNA (118-MER)


Mass: 37992.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#85: RNA chain RNA (1743-MER)


Mass: 564635.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

+
30S ribosomal protein ... , 3 types, 3 molecules BhBtBo

#47: Protein 30S ribosomal protein S9, mitochondrial


Mass: 48058.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8L6Z4
#56: Protein 30S ribosomal protein S31, mitochondrial


Mass: 10978.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SJU8
#67: Protein 30S ribosomal protein S16-2, chloroplastic/mitochondrial


Mass: 15126.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LTS6

+
40S ribosomal protein ... , 3 types, 3 molecules BiBrBg

#48: Protein 40S ribosomal protein S10, mitochondrial


Mass: 27135.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P42797
#51: Protein 40S ribosomal protein S19, mitochondrial


Mass: 23675.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P39697
#64: Protein 40S ribosomal protein S15a-5


Mass: 14941.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M0E0

+
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: The large mitoribosomal subunit of the Plant mitoribosome
Type: RIBOSOME
Entity ID: #1, #10-#19, #2, #20-#29, #3, #30-#39, #4, #40-#49, #5, #50-#59, #6, #60-#69, #7, #70-#79, #8, #80-#89, #9
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 / Cs: 2.7 mm / C2 aperture diameter: 30 µm
Image recordingAverage exposure time: 1 sec. / Electron dose: 3 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1

-
Processing

EM software
IDNameVersionCategory
1RELION3.0.7particle selection
4Gctf1.06CTF correction
7Coot0.9model fitting
9PHENIXmodel refinement
10RELION3.0.7initial Euler assignment
11RELION3.0.7final Euler assignment
12RELION3.0.7classification
13RELION3.0.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65280 / Num. of class averages: 4 / Symmetry type: POINT

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