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- EMDB-27249: Yeast mitochondrial small subunit assembly intermediate (State 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-27249
TitleYeast mitochondrial small subunit assembly intermediate (State 1)Mitochondrion
Map dataFull map
Sample
  • Complex: Yeast mitochondrial small subunit assembly intermediate (State 3)Mitochondrion
    • Protein or peptide: x 15 types
    • RNA: x 1 types
  • Ligand: x 2 types
Function / homology
Function and homology information


mitochondrial small ribosomal subunit / mitochondrial translation / sporulation resulting in formation of a cellular spore / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / methylation / mitochondrial inner membrane ...mitochondrial small ribosomal subunit / mitochondrial translation / sporulation resulting in formation of a cellular spore / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / methylation / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / translation / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein S22, mitochondrial, budding yeast / Ribosomal protein S35, mitochondrial / Ribosomal protein Rsm22-like / Mitochondrial small ribosomal subunit Rsm22 / Eukaryotic mitochondrial regulator protein / IGR protein motif / Protein Fyv4 / IGR protein motif / IGR / PPR repeat family ...Ribosomal protein S22, mitochondrial, budding yeast / Ribosomal protein S35, mitochondrial / Ribosomal protein Rsm22-like / Mitochondrial small ribosomal subunit Rsm22 / Eukaryotic mitochondrial regulator protein / IGR protein motif / Protein Fyv4 / IGR protein motif / IGR / PPR repeat family / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / Ribosomal protein S17/S11 / Ribosomal protein S4 signature. / Ribosomal_S15 / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal protein S12/S23 / S4 RNA-binding domain profile. / Ribosomal protein S12/S23 / Ribosomal protein S17 / Ribosomal protein S15 / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S12 signature. / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
MRPS12 isoform 1 / CCM1 isoform 1 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein uS4m / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein uS5m / Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial / Small ribosomal subunit protein mS41 ...MRPS12 isoform 1 / CCM1 isoform 1 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein uS4m / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein uS5m / Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial / Small ribosomal subunit protein mS41 / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS45 / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS8m
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBurnside C / Harper N / Klinge S
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM136640-02 United States
CitationJournal: Nature / Year: 2023
Title: Principles of mitoribosomal small subunit assembly in eukaryotes.
Authors: Nathan J Harper / Chloe Burnside / Sebastian Klinge /
Abstract: Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is ...Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism. Here we used cryo-electron microscopy to determine nine structures of native yeast and human mitoribosomal small subunit assembly intermediates, illuminating the mechanistic basis for how GTPases are used to control early steps of decoding centre formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins have active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins and rRNA that are required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies.
History
DepositionJun 8, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27249.png

Downloads & links

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Map

FileDownload / File: emd_27249.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Voxel sizeX=Y=Z: 1.057 Å
Density
Contour LevelBy AUTHOR: 4.3
Minimum - Maximum-10.443467 - 27.062866
Average (Standard dev.)0.027765708 (±1.0685806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 422.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27249_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27249_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_27249_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast mitochondrial small subunit assembly intermediate (State 3)

EntireName: Yeast mitochondrial small subunit assembly intermediate (State 3)Mitochondrion
Components
  • Complex: Yeast mitochondrial small subunit assembly intermediate (State 3)Mitochondrion
    • Protein or peptide: Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial
    • Protein or peptide: 37S ribosomal protein MRP13, mitochondrialRibosome
    • Protein or peptide: Mitochondrial group I intron splicing factor CCM1
    • Protein or peptide: 37S ribosomal protein S28, mitochondrialRibosome
    • Protein or peptide: 37S ribosomal protein S16, mitochondrialRibosome
    • Protein or peptide: 37S ribosomal protein S17, mitochondrialRibosome
    • Protein or peptide: 37S ribosomal protein RSM18, mitochondrialRibosome
    • Protein or peptide: 37S ribosomal protein PET123, mitochondrialRibosome
    • Protein or peptide: Protein FYV4, mitochondrial
    • Protein or peptide: 37S ribosomal protein NAM9, mitochondrialRibosome
    • Protein or peptide: 37S ribosomal protein S5, mitochondrialRibosome
    • Protein or peptide: 37S ribosomal protein MRP17, mitochondrialRibosome
    • Protein or peptide: 37S ribosomal protein S35, mitochondrialRibosome
    • Protein or peptide: 37S ribosomal protein S8, mitochondrialRibosome
    • RNA: 15S ribosomal RNA
    • Protein or peptide: uS12m
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Yeast mitochondrial small subunit assembly intermediate (State 3)

SupramoleculeName: Yeast mitochondrial small subunit assembly intermediate (State 3)
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.26 MDa

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Macromolecule #1: Probable S-adenosyl-L-methionine-dependent RNA methyltransferase ...

MacromoleculeName: Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 72.308328 KDa
SequenceString: MMKRCFSILP QNVRFSSKFT SLNLPKLDLA DFIDSNKRGI NVLPSYRDET ASTTQATNSK ELRLLSKTLQ GQSYRDQLEL NPDVSKAIN NNIMAVHIPN NLRRVATNYY KEIQEPNSLH RPCRTKMEVD AHIASIFLQN YGSIFQSLKE LQKRVGPDNF K PQRILDVG ...String:
MMKRCFSILP QNVRFSSKFT SLNLPKLDLA DFIDSNKRGI NVLPSYRDET ASTTQATNSK ELRLLSKTLQ GQSYRDQLEL NPDVSKAIN NNIMAVHIPN NLRRVATNYY KEIQEPNSLH RPCRTKMEVD AHIASIFLQN YGSIFQSLKE LQKRVGPDNF K PQRILDVG YGPATGIVAL NDILGPNYRP DLKDAVILGN AEMQERAKII LSRQLNEVVD TVEENVSTEK EQETDRRNKN FQ EDEHIGE VMTKKINIMT NLRSSIPASK EYDLIILTHQ LLHDGNQFPI QVDENIEHYL NILAPGGHIV IIERGNPMGF EII ARARQI TLRPENFPDE FGKIPRPWSR GVTVRGKKDA ELGNISSNYF LKVIAPCPHQ RKCPLQVGNP NFYTHKEGKD LKFC NFQKS IKRPKFSIEL KKGKLLATSW DGSQGNASRL KGTGRRNGRD YEILNYSYLI FERSHKDENT LKEIKKLRNE NVNGK YDIG SLGDDTQNSW PRIINDPVKR KGHVMMDLCA PSGELEKWTV SRSFSKQIYH DARKSKKGDL WASAAKTQIK GLGDLN VKK FHKLEKERIK QLKKEERQKA RKAMESYNEL EDSLQFDDHQ FSNFEVMKKL STFHGNDFLQ HVNRK

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Macromolecule #2: 37S ribosomal protein MRP13, mitochondrial

MacromoleculeName: 37S ribosomal protein MRP13, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 39.045031 KDa
SequenceString: MGTITVVINE GPILLIRALH RATTNKKMFR STVWRRFAST GEIAKAKLDE FLIYHKTDAK LKPFIYRPKN AQILLTKDIR DPKTREPLQ PRPPVKPLSK QTLNDFIYSV EPNSTELLDW FKEWTGTSIR KRAIWTYISP IHVQKMLTAS FFKIGKYAHM V GLLYGIEH ...String:
MGTITVVINE GPILLIRALH RATTNKKMFR STVWRRFAST GEIAKAKLDE FLIYHKTDAK LKPFIYRPKN AQILLTKDIR DPKTREPLQ PRPPVKPLSK QTLNDFIYSV EPNSTELLDW FKEWTGTSIR KRAIWTYISP IHVQKMLTAS FFKIGKYAHM V GLLYGIEH KFLKAQNPSV FDIEHFFNTN IMCALHRNRL KDYKDAEIAQ RKLQVAWKKV LNRKNNTGLA NILVATLGRQ IG FTPELTG LQPVDISLPD IPNSSSGAEL KDLLSKYEGI YLIARTLLDI DQHNAQYLEL QEFIRQYQNA LSESSDPYDT HLK ALGLLE TPPPQESTEK EEK

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Macromolecule #3: Mitochondrial group I intron splicing factor CCM1

MacromoleculeName: Mitochondrial group I intron splicing factor CCM1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 101.568547 KDa
SequenceString: MYMARCGPKN NVLCFPFQLS FLFSKRLINK RFKYTLQTED EKNMMGSLSK NKIITPEDVE FKLAQLREFS NTLKERIHNT KSVNSDGHQ SNSIAPISED SRNVNVTKTS SVPNEEKSKN LSDLIHSSFL EKMDHLVPKV IRERVADDDI LAKNLFDRSH S NWAPVIDR ...String:
MYMARCGPKN NVLCFPFQLS FLFSKRLINK RFKYTLQTED EKNMMGSLSK NKIITPEDVE FKLAQLREFS NTLKERIHNT KSVNSDGHQ SNSIAPISED SRNVNVTKTS SVPNEEKSKN LSDLIHSSFL EKMDHLVPKV IRERVADDDI LAKNLFDRSH S NWAPVIDR LYVSEKRFMD IDSREFSVWL NGTVKYLPFH SILHLDEMLL EQINGDVVKF NTHMYECIFN NLGNLKPTNF NQ DGTNDKV ILKMKELLER YDKALKITEE RINKKEGFPS KVPKMTQAIL NNCLKYSTKC SSFHDMDYFI TKFRDDYGIT PNK QNLTTV IQFYSRKEMT KQAWNTFDTM KFLSTKHFPD ICTYNTMLRI CEKERNFPKA LDLFQEIQDH NIKPTTNTYI MMAR VLASS SSNAVVSEGK SDSLRLLGWK YLHELEDKNL YRHKKDDLNL FLAMMALAAF DGDIELSRAL YYLFIAKKYK TLCAN WKGN ILVDQDTIWK STLMPEMLNY LMLAYARFDP RNLPVLSGYE KGIELRRKFL REFDSSMRLD DTDKLVKFKL PFLPIS DLN SEAQVLAESN AIWSFNMENG GTRNTLTSSN EAALEDIKKY RQLLDSFAQE AEDFNEFKFK VMYEVTKMQR ESINVNV FN KISLHTYLSI PINLKQQKEF LRRLTFFTFQ QHEFEAVIKR LYEGYRNIPS SHTRDQNSIS TEAISVSKPE TTEDLNLI M HDIWYITCLR HKIMMDTTLY ELVMKAAIEF QNEDLAKKVW NDRGKFRTTV PFLKMDQRIR IAKDQKFAHL MVEFFTKQG KYSDAIAIIL SSKNRFNWTY SMVRNLHKAL EEIEDRNSVE ILLDVVNKKS HAKALKWEEQ ELNM

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Macromolecule #4: 37S ribosomal protein S28, mitochondrial

MacromoleculeName: 37S ribosomal protein S28, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 33.116383 KDa
SequenceString: MSIVGRNAIL NLRISLCPLF MGKRSFVSSP VSNSAKAVKF LKAQRRKQKN EAKQATLKAS TDKVDPVLGR ADTPFITRIM AELKEPLVL SKGYNIEEVD KFLAAIESAK RERAELSGLN TEVVGIEDIE KLEDRREAIL RILSMRNSEN KNAIKMAVEL A RKEFERFP ...String:
MSIVGRNAIL NLRISLCPLF MGKRSFVSSP VSNSAKAVKF LKAQRRKQKN EAKQATLKAS TDKVDPVLGR ADTPFITRIM AELKEPLVL SKGYNIEEVD KFLAAIESAK RERAELSGLN TEVVGIEDIE KLEDRREAIL RILSMRNSEN KNAIKMAVEL A RKEFERFP GDTGSSEVQA ACMTVRIQNM ANHIKEHRKD FANTRNLRIL VQQRQAILRY LKRDNPEKYY WTIQKLGLND AA ITDEFNM DRRYMQDYEF FGDKILIRDS KKVANQKRKE IRKQKRATF

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Macromolecule #5: 37S ribosomal protein S16, mitochondrial

MacromoleculeName: 37S ribosomal protein S16, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 13.663011 KDa
SequenceString:
MTCGLVRIRL ARFGRKNSPV YNIVVANSRK ARDAKPIEVL GTYVPVPSPV TKRELKRGVV PIKDVKLDFD RTKYWIGVGA QPSETVTKL LRKAGILNDA WATSKNSNVN RKVVFERMET LE

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Macromolecule #6: 37S ribosomal protein S17, mitochondrial

MacromoleculeName: 37S ribosomal protein S17, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.683986 KDa
SequenceString: MARQNFLGLV VSQGKMQKTV KVRVETKVFN KKINKELFHR RDYLVHDEGE ISREGDLVRI EATRPLSKRK FFAIAEIIRN KGQQFALYE SEAQLSVAKE EAQKAKEFLD KRSVRENKLN EKTTLLRDIR TIQDALSSGS TPKELLEIKQ RYGIQDFSQE T VRQLLQLD ...String:
MARQNFLGLV VSQGKMQKTV KVRVETKVFN KKINKELFHR RDYLVHDEGE ISREGDLVRI EATRPLSKRK FFAIAEIIRN KGQQFALYE SEAQLSVAKE EAQKAKEFLD KRSVRENKLN EKTTLLRDIR TIQDALSSGS TPKELLEIKQ RYGIQDFSQE T VRQLLQLD ISGLEVNLEK QRSLIDRIQT RLSELLSNDL KCDQFLKDHG VEDPLTLKKN IKKNLLRKHV MMDMQQPSQ

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Macromolecule #7: 37S ribosomal protein RSM18, mitochondrial

MacromoleculeName: 37S ribosomal protein RSM18, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.86649 KDa
SequenceString:
MQPIIKGAVS STFKRALYNF GIKEKKSVNI EMGRTQQTKK IDQSLSKKLP KGTIYDPFDF SMGRIHLDRK YQANKNSNRN DIMKSGANP LEFYARPRIL SRYVTSTGRI QHRDITGLSA KNQRRLSKAI RRCQAIGLM

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Macromolecule #8: 37S ribosomal protein PET123, mitochondrial

MacromoleculeName: 37S ribosomal protein PET123, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 36.059281 KDa
SequenceString: MGKGAAKYGF KSGVFPTTRS ILKSPTTKQT DIINKVKSPK PKGVLGIGYA KGVKHPKGSH RLSPKVNFID VDNLIAKTVA EPQSIKSSN GSAQKVRLQK AELRRKFLIE AFRKEEARLL HKHEYLQKRT KELEKAKELE LEKLNKEKSS DLTIMTLDKM M SQPLLRNR ...String:
MGKGAAKYGF KSGVFPTTRS ILKSPTTKQT DIINKVKSPK PKGVLGIGYA KGVKHPKGSH RLSPKVNFID VDNLIAKTVA EPQSIKSSN GSAQKVRLQK AELRRKFLIE AFRKEEARLL HKHEYLQKRT KELEKAKELE LEKLNKEKSS DLTIMTLDKM M SQPLLRNR SPEESELLKL KRNYNRSLLN FQAHKKKLNE LLNLYHVANE FIVTESQLLK KIDKVFNDET EEFTDAYDVT SN FTQFGNR KLLLSGNTTL QTQINNAIMG SLSNEKFFDI SLVDSYLNKD LKNISNKIDS KLNPTSNGAG NNGNNNNTTN L

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Macromolecule #9: Protein FYV4, mitochondrial

MacromoleculeName: Protein FYV4, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.321684 KDa
SequenceString:
MIPSRISHKF PLFLRSSLAA PKAAYRFSST IPKPSDQVPD VDAFLNKIGR NCNELKDTFE NNWNNLFQWD SKILKEKGVN IQQRKYILK QVHNYRNNRP IHEIKLGKKS FFGGERKRKA FTAKWKAENK Q

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Macromolecule #10: 37S ribosomal protein NAM9, mitochondrial

MacromoleculeName: 37S ribosomal protein NAM9, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 56.450949 KDa
SequenceString: MPRKANLLKS LARGRVRTSF NKYNLFNLYK KGGVDLKSKS LYQQKWTAKQ ETRAYHGEHL TEKRWQTVFK PKLDSVAQLD ASLRGGEIK ETPFLLQTFA VLEKRLDFAL FRAMFASSVR QARQFILHGN VRVNGVKIKH PSYTLKPGDM FSVKPDKVLE A LGAKKPSF ...String:
MPRKANLLKS LARGRVRTSF NKYNLFNLYK KGGVDLKSKS LYQQKWTAKQ ETRAYHGEHL TEKRWQTVFK PKLDSVAQLD ASLRGGEIK ETPFLLQTFA VLEKRLDFAL FRAMFASSVR QARQFILHGN VRVNGVKIKH PSYTLKPGDM FSVKPDKVLE A LGAKKPSF QEALKIDKTQ IVLWNKYVKE AKTEPKEVWE KKLENFEKMS DSNPKKLQFQ EFLRQYNKNL ESQQYNALKG CT QEGILRK LLNVEKEIGK SNNEPLSIDE LKQGLPEIQD SQLLESLNNA YQEFFKSGEI RREIISKCQP DELISLATEM MNP NETTKK ELSDGAKSAL RSGKRIIAES VKLWTKNITD HFKTRMSDIS DGSLTFDPKW AKNLKYHDPI KLSELEGDEP KARK LINLP WQKNYVYGRQ DPKKPFFTPW KPRPFLSPFA ILPHHLEISF KTCHAVYLRD PVARPGQSEV ISPFDVPVHE RAYMY YLRN GK

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Macromolecule #11: 37S ribosomal protein S5, mitochondrial

MacromoleculeName: 37S ribosomal protein S5, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 34.941102 KDa
SequenceString: MFKRQLSTSV RYLQHYDESL LSRYYPESLL KSIKLAQQTI PEDTKFRVSR NVEFAPPYLD DFTKIHPFWD YKPGMPHLHA QEENNNFSI FRWDQVQQPL PGEGNILPPG VSLPNDGGRK SKSADVAAGL HKQTGVDPDY ITRKLTMKPL VMKRVSNQTG K GKIASFYA ...String:
MFKRQLSTSV RYLQHYDESL LSRYYPESLL KSIKLAQQTI PEDTKFRVSR NVEFAPPYLD DFTKIHPFWD YKPGMPHLHA QEENNNFSI FRWDQVQQPL PGEGNILPPG VSLPNDGGRK SKSADVAAGL HKQTGVDPDY ITRKLTMKPL VMKRVSNQTG K GKIASFYA LVVVGDKNGM VGLGEGKSRE EMSKAIFKAH WDAVRNLKEI PRYENRTIYG DIDFRYHGVK LHLRSAKPGF GL RVNHVIF EICECAGIKD LSGKVYKSRN DMNIAKGTIE AFTKAQKTLD EVALGRGKKL VDVRKVYYSS

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Macromolecule #12: 37S ribosomal protein MRP17, mitochondrial

MacromoleculeName: 37S ribosomal protein MRP17, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.046702 KDa
SequenceString:
MLYELIGLVR ITNSNAPKLE AKELSSTIGK LIIQNRGVVR DIVPMGIRYL PKIMKKDQEK HFRAYHFLML FDSSAAVQSE ILRTLKKDP RVIRSSIVKV DLDKQLDRAS SLHRSLGKKS ILELVNEDYQ SI

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Macromolecule #13: 37S ribosomal protein S35, mitochondrial

MacromoleculeName: 37S ribosomal protein S35, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 39.638172 KDa
SequenceString: MSYGLTGTSS KLRGTSSIFS WTQVRHFSRR RIAYPFYPFK KLGRQHPKKH DTNLKTAMRQ FLGPKNYKGE YVMNKYFTVP TNHVPNYIK PDLERGQSLE HPVTKKPLQL RYDGTLGPPP VENKRLQNIF KDRLLQPFPS NPHCKTNYVL SPQLKQSIFE E ITVEGLSA ...String:
MSYGLTGTSS KLRGTSSIFS WTQVRHFSRR RIAYPFYPFK KLGRQHPKKH DTNLKTAMRQ FLGPKNYKGE YVMNKYFTVP TNHVPNYIK PDLERGQSLE HPVTKKPLQL RYDGTLGPPP VENKRLQNIF KDRLLQPFPS NPHCKTNYVL SPQLKQSIFE E ITVEGLSA QQVSQKYGLK IPRVEAIVKL VSVENSWNRR NRVSSDLKTM DETLYRMFPV FDSDASFKRE NLSEIPVPQK TL ASRFLTI AESEPFGPVD AAHVLELEPA VETLRNLSTV GEHSSGHQQS TNKNTKVIYG ELVEGERSQY KFTNAKVGKV GYR YGSGNR DNKKDRRIGF NKLGQMVYI

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Macromolecule #14: 37S ribosomal protein S8, mitochondrial

MacromoleculeName: 37S ribosomal protein S8, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.496602 KDa
SequenceString:
MSLVKLANTC AHLQNCSKVR VALTSIPYTK LQLQFAYNLY QQGFLSSLQK GSTMGPDKDF VEVTPDNIST RRLWVGLKYR DNKPVLSSC KLISKPNSRI HLPMEDMKKL CSGVTIRNIK PLQPGELILV RAHNNIMDIN EAISKKLDGE VLCRVK

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Macromolecule #16: uS12m

MacromoleculeName: uS12m / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 16.94874 KDa
SequenceString:
MLSRFMSNTW CTPLRQAQRL FSSTTTMQAT LNQIKRGSGP PRRKKISTAP QLDQCPQRKG VVLRVMVLKP KKPNSAQRKA CRVRLTNGN VVSAYIPGEG HDAQEHSIVY VRGGRCQDLP GVKYHVIRGA GDLSGVVNRI SSRSKYGAKK PSKS

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Macromolecule #15: 15S ribosomal RNA

MacromoleculeName: 15S ribosomal RNA / type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 549.234062 KDa
SequenceString: UUUUAUAUAA UAAUAAUAAU AUAUAUAUAU AUAUAUUAUU AUAUUAGUUA UAUAAUAAGG AAAAGUAAAA AAUUUAUAAG AAUAUGAUG UUGGUUCAGA UUAAGCGCUA AAUAAGGACA UGACACAUGC GAAUCAUACG UUUAUUAUUG AUAAGAUAAU A AAUAUGUG ...String:
UUUUAUAUAA UAAUAAUAAU AUAUAUAUAU AUAUAUUAUU AUAUUAGUUA UAUAAUAAGG AAAAGUAAAA AAUUUAUAAG AAUAUGAUG UUGGUUCAGA UUAAGCGCUA AAUAAGGACA UGACACAUGC GAAUCAUACG UUUAUUAUUG AUAAGAUAAU A AAUAUGUG GUGUAAACGU GAGUAAUUUU AUUAGGAAUU AAUGAACUAU AGAAUAAGCU AAAUACUUAA UAUAUUAUUA UA UAAAAAU AAUUUAUAUA AUAAAAAGGA UAUAUAUAUA AUAUAUAUUU AUCUAUAGUC AAGCCAAUAA UGGUUUAGGU AGU AGGUUU AUUAAGAGUU AAACCUAGCC AACGAUCCAU AAUCGAUAAU GAAAGUUAGA ACGAUCACGU UGACUCUGAA AUAU AGUCA AUAUCUAUAA GAUACAGCAG UGAGGAAUAU UGGACAAUGA UCGAAAGAUU GAUCCAGUUA CUUAUUAGGA UGAUA UAUA AAAAUAUUUU AUUUUAUUUA UAAAUAUUAA AUAUUUAUAA UAAUAAUAAU AAUAAUAUAU AUAUAUAAAU UGAUUA AAA AUAAAAUCCA UAAAUAAUUA AAAUAAUGAU AUUAAUUACC AUAUAUAUUU UUAUAUGGAU AUAUAUAUUA AUAAUAA UA UUAAUUUUAU UAUUAUUAAU AAUAUAUUUU AAUAGUCCUG ACUAAUAUUU GUGCCAGCAG UCGCGGUAAC ACAAAGAG G GCGAGCGUUA AUCAUAAUGG UUUAAAGGAU CCGUAGAAUG AAUUAUAUAU UAUAAUUUAG AGUUAAUAAA AUAUAAUUA AAGAAUUAUA AUAGUAAAGA UGAAAUAAUA AUAAUAAUUA UAAGACUAAU AUAUGUGAAA AUAUUAAUUA AAUAUUAACU GACAUUGAG GGAUUAAAAC UAGAGUAGCG AAACGGAUUC GAUACCCGUG UAGUUCUAGU AGUAAACUAU GAAUACAAUU A UUUAUAAU AUAUAUUAUA UAUAAAUAAU AAAUGAAAAU GAAAGUAUUC CACCUGAAGA GUACGUUAGC AAUAAUGAAA CU CAAAACA AUAGACGGUU ACAGACUUAA GCAGUGGAGC AUGUUAUUUA AUUCGAUAAU CCACGACUAA CCUUACCAUA UUU UGAAUA UUAUAAUAAU UAUUAUAAUU AUUAUAUUAC AGGCGUUACA UUGUUGUCUU UAGUUCGUGC UGCAAAGUUU UAGA UUAAG UUCAUAAACG AACAAAACUC CAUAUAUAUA AUUUUAAUUA UAUAUAAUUU UAUAUUAUUU AUUAAUAUAA AGAAA GGAA UUAAGACAAA UCAUAAUGAU CCUUAUAAUA UGGGUAAUAG ACGUGCUAUA AUAAAAUGAU AAUAAAAUUA UAUAAA AUA UAUUUAAUUA UAUUUAAUUA AUAAUAUAAA ACAUUUUAAU UUUUAAUAUA UUUUUUUAUU AUAUAUUAAU AUGAAUU AU AAUCUGAAAU UCGAUUAUAU GAAAAAAGAA UUGCUAGUAA UACGUAAAUU AGUAUGUUAC GGUGAAUAUU CUAACUGU U UCGCACUAAU CACUCAUCAC GCGUUGAAAC AUAUUAUUAU CUUAUUAUUU AUAUAAUAUU UUUUAAUAAA UAUUAAUAA UUAUUAAUUU AUAUUUAUUU AUAUCAGAAA UAAUAUGAAU UAAUGCGAAG UUGAAAUACA GUUACCGUAG GGGAACCUGC GGUGGGCUU AUAAAUAUCU UAAAUAUUCU UACA

+
Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 29 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 14111 / Average electron dose: 61.73 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3286640
Startup modelType of model: OTHER / Details: Ab Initio (Cryosparc)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.19) / Number images used: 19720
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5mrc

RefinementSpace: REAL
Output model

PDB-8d8j:
Yeast mitochondrial small subunit assembly intermediate (State 1)

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