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- EMDB-56961: Map of the 50S ribosomal subunit with E-tRNA and RsfS from the al... -

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Basic information

Entry
Database: EMDB / ID: EMD-56961
TitleMap of the 50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi
Map dataSharpened map of the Asaia 50S ribosomal subunit
Sample
  • Complex: Structure of the 50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi
    • Protein or peptide: x 27 types
    • RNA: x 3 types
KeywordsRibosome / 50S / RsfS
Biological speciesAsaia platycodi JCM 25414 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsChan LI / Omae K / Amikura K / Suzuki S / Melnikov SM
Funding support United Kingdom, Japan, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008695/1 United Kingdom
Royal SocietyICA/R2/242249 United Kingdom
Japan Science and TechnologyJPMJCR20S4 Japan
CitationJournal: BioRXiv / Year: 2025
Title: The Evolutionary Lifecycle of Ribosome Hibernation Factors
Authors: Chan LI / Melnikov SV
History
DepositionFeb 27, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56961.png

Downloads & links

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Map

FileDownload / File: emd_56961.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of the Asaia 50S ribosomal subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.166
Minimum - Maximum-1.0315642 - 1.7155675
Average (Standard dev.)0.0004824559 (±0.07066611)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of the Asaia 50S ribosomal subunit

Fileemd_56961_additional_1.map
AnnotationUnsharpened map of the Asaia 50S ribosomal subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B for Asaia 50S ribosomal subunit

Fileemd_56961_half_map_1.map
AnnotationHalf map B for Asaia 50S ribosomal subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A for Asaia 50S ribosomal subunit

Fileemd_56961_half_map_2.map
AnnotationHalf map A for Asaia 50S ribosomal subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the 50S ribosomal subunit with E-tRNA and RsfS from ...

EntireName: Structure of the 50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi
Components
  • Complex: Structure of the 50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi
    • Protein or peptide: Large ribosomal subunit protein bL36
    • Protein or peptide: Large ribosomal subunit protein uL2
    • RNA: 23S rRNA
    • Protein or peptide: Large ribosomal subunit protein bL35
    • Protein or peptide: Large ribosomal subunit protein bL34
    • Protein or peptide: Large ribosomal subunit protein bL33
    • Protein or peptide: Large ribosomal subunit protein bL32
    • Protein or peptide: Large ribosomal subunit protein uL30
    • Protein or peptide: Large ribosomal subunit protein uL29
    • Protein or peptide: Large ribosomal subunit protein bL28
    • Protein or peptide: Large ribosomal subunit protein bL27
    • Protein or peptide: Large ribosomal subunit protein bL25
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Large ribosomal subunit protein bL21
    • Protein or peptide: Large ribosomal subunit protein bL20
    • Protein or peptide: Large ribosomal subunit protein bL17
    • Protein or peptide: Large ribosomal subunit protein uL16
    • Protein or peptide: Large ribosomal subunit protein uL15
    • Protein or peptide: Large ribosomal subunit protein uL14
    • Protein or peptide: Large ribosomal subunit protein uL13
    • Protein or peptide: Large ribosomal subunit protein bL9
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: Large ribosomal subunit protein uL4
    • Protein or peptide: Large ribosomal subunit protein uL3
    • RNA: E-site tRNA (heterogeneous fragment modelled as poly-U with the CCA-end)
    • RNA: 5S rRNA (fragment)
    • Protein or peptide: Large ribosomal subunit protein bL19
    • Protein or peptide: Ribosome silencing factor S

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Supramolecule #1: Structure of the 50S ribosomal subunit with E-tRNA and RsfS from ...

SupramoleculeName: Structure of the 50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)

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Macromolecule #1: Large ribosomal subunit protein bL36

MacromoleculeName: Large ribosomal subunit protein bL36 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 4.943022 KDa
SequenceString:
MKIRNSLKSA KLRDKDCRVV RRRGRVYVIN KKNPRMKARQ G

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Macromolecule #2: Large ribosomal subunit protein uL2

MacromoleculeName: Large ribosomal subunit protein uL2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 30.385871 KDa
SequenceString: MALKHFNPTT PSTRGTVLID RSELYKGKPV KQLTEGKNKT GGRNNHGRTT SRFRGGGHKQ SYRYVDFKRR KFDVAGIVER LEYDPNRTA FIALIKYEDG ELAYILAPQR VKVGDQVIAG ERTDVKPGNA MPLGSMPVGT IVHNIELKPG AGGKIARSAG T YCQLVGKD ...String:
MALKHFNPTT PSTRGTVLID RSELYKGKPV KQLTEGKNKT GGRNNHGRTT SRFRGGGHKQ SYRYVDFKRR KFDVAGIVER LEYDPNRTA FIALIKYEDG ELAYILAPQR VKVGDQVIAG ERTDVKPGNA MPLGSMPVGT IVHNIELKPG AGGKIARSAG T YCQLVGKD AGYAQVKLQS GELRLVRGEC MATVGAVSNP DNMNQHLGKA GRNRWLGRRP HNRGVVMNPV DHPHGGGEGR TS GGRHPVT PWGKPTKGYK TRVNKKTDSL IIRRRKTGK

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Macromolecule #4: Large ribosomal subunit protein bL35

MacromoleculeName: Large ribosomal subunit protein bL35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 7.580134 KDa
SequenceString:
MPKMKTKSSV KKRFKITATG KVMCGPGNKR HGLINRPQKM KRTNRGPQTM TDMDAKTVKQ WAPYGLA

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Macromolecule #5: Large ribosomal subunit protein bL34

MacromoleculeName: Large ribosomal subunit protein bL34 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 5.270342 KDa
SequenceString:
MKRTYQPSKL VRKRRHGFRA RMETVGGRRV INNRRAKGRK KLSA

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Macromolecule #6: Large ribosomal subunit protein bL33

MacromoleculeName: Large ribosomal subunit protein bL33 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 6.330472 KDa
SequenceString:
MAKSNVIQIR LVSTAETGYF YVTKKNARSA TGKMEVRKYD PVVRKHVAFR EAKIK

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Macromolecule #7: Large ribosomal subunit protein bL32

MacromoleculeName: Large ribosomal subunit protein bL32 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 7.436685 KDa
SequenceString:
MAVPKRKTTP SRMGMRRSHH ALTVQAHAEC SNCGELKRPH HVCAHCGHYD GREVVASGKT LKTTVRV

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Macromolecule #8: Large ribosomal subunit protein uL30

MacromoleculeName: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 6.549607 KDa
SequenceString:
MAENKTVRVK QIASAIGRKP GQADTLVGLG LRGIGSEREL EDTPSVRGMI RKVAHLIQVE G

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Macromolecule #9: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 8.423673 KDa
SequenceString:
MADAYKVADL RAKSADELDA LLLDLKREQL NLRFQAATGQ SEGVGRVRVL RRAIARIKTV AHQSKNKVGA KTSTAES

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Macromolecule #10: Large ribosomal subunit protein bL28

MacromoleculeName: Large ribosomal subunit protein bL28 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 11.121853 KDa
SequenceString:
MSRRCQITGK GVLTGNNVSH ANNKTRRRFL PNLQEITLLS DILGTGVRLR LSTQGIRTVE HNGGLDSFLI TTPNRKLPVE AQVIKRRIL RAQESKAAQT A

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Macromolecule #11: Large ribosomal subunit protein bL27

MacromoleculeName: Large ribosomal subunit protein bL27 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 9.183541 KDa
SequenceString:
MAQKKAGGSS RNGRDSAGRR LGVKKFGGEA VIAGNIIVRQ RGTKMMAGSN VGVGRDHTLF ALADGAVKFT RRAEGRVHVS VTLAEAAE

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Macromolecule #12: Large ribosomal subunit protein bL25

MacromoleculeName: Large ribosomal subunit protein bL25 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 22.683055 KDa
SequenceString: MTNMTSLEVS TRAKAGKGAA RATRRAGLVP GVVYGGKQEP ALIQIDPRII HKEMVRGGWR SRLFELPLEG GTVRALLREV QLHPVTDAP IHVDFQRLAA GEKVHVTVSI HVTGEDKAPG IKRGGVLNLV RHTVDVMADV DSIPASFTVD LSALDIHDNV R WDDLTGTE ...String:
MTNMTSLEVS TRAKAGKGAA RATRRAGLVP GVVYGGKQEP ALIQIDPRII HKEMVRGGWR SRLFELPLEG GTVRALLREV QLHPVTDAP IHVDFQRLAA GEKVHVTVSI HVTGEDKAPG IKRGGVLNLV RHTVDVMADV DSIPASFTVD LSALDIHDNV R WDDLTGTE NVTPVLQLPN FVIATIAPPT VDAEMEAEAA AKAAAEAAAP AKKK

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Macromolecule #13: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 11.483583 KDa
SequenceString:
MAARIKKGDQ VLVLSGSSRG TRGEVLAVLP KVEKAIVRGV AVAKRHQKPT RMNQEGGIIA KEMPVHLSNL KLVDPKSGKP TRVGFRQLE DGRKVRVAKV TGEVIEG

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Macromolecule #14: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 12.48085 KDa
SequenceString:
MTTSIVLARR NKALRMTRES MFDIVRAPLI TEKATALSER NQVVFRVAMT AAKPEIKVAV ETLFGVKVVS VNTLVQKGKT KMVKGRPGR RSDIKKAYVQ LAEGQSIDLT AKLG

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Macromolecule #15: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 15.759271 KDa
SequenceString:
MSKPKHIRTL ADTEAQAVAR NIRVSPRKLN LVAAMIRNQP ADKAIAALTF SRRRIAQEVR KALESAVANA ENNHQLDVDQ LVVKTAEVG KSIVMKRFHA RGRGRSSRIE KFFSHLKIVV AERAAEEAPA PKGKGKDAAE QKAA

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Macromolecule #16: Large ribosomal subunit protein bL21

MacromoleculeName: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 11.301121 KDa
SequenceString:
MFAVIRTGGK QYRVTPQITL KVEKLEAEAG TTITFSDVLA VGSDAGIKIG APLVAGATVT ATVIAQDRLD TVIIFKKRRR QNSRRKNGH RQHVTVLRID AINAA

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Macromolecule #17: Large ribosomal subunit protein bL20

MacromoleculeName: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 14.604923 KDa
SequenceString:
MARVKRGVTT HARHKKVLDL AKGYRGRSST NYRIALERVE KALRYAYRDR RNKKRDFRAL WIQRINAAVR EQGLTYSKFI NGLAKAGIE IDRKVLAAIA FDDAATFAEI VKLAQMALDL PAEEQTAQA

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Macromolecule #18: Large ribosomal subunit protein bL17

MacromoleculeName: Large ribosomal subunit protein bL17 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 15.573997 KDa
SequenceString:
MRHGVAGRKL NVTSTHRAAM FRNMAVAIIK HEQITTTLPK AKEIRPVVEK LITLGKRGTL HARRQAFAQL RDETIVTKLF STIAERYQG RSGGYTRVLK AGVRYGDNAD MAVVEMVDRD VDAKGKDSGP VINQSGEEPM AA

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Macromolecule #19: Large ribosomal subunit protein uL16

MacromoleculeName: Large ribosomal subunit protein uL16 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 15.212047 KDa
SequenceString:
MLSPKRTKFR KAHKGRIHGL AKGGTTLNFG AFGLKALEPE RITARQIEAS RRAITRAMKR AGRVWIRIFP DLPVSTKPAE VRMGSGKGS PEFWVARVKP GRVLFEIEGV PPEVAREALA LGAAKLPIKT KFITRIGEA

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Macromolecule #20: Large ribosomal subunit protein uL15

MacromoleculeName: Large ribosomal subunit protein uL15 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 16.795334 KDa
SequenceString:
MNLNELRDNA GARYRKKRLG RGIGSGKGKT SGRGVKGQKA REGVSLNGFE GGQLPLYRRM PKRGFKNIFR KEFAPVNLGA IDRALADGK LQADATITEE TLRAAGLVGT GKYAGIRLLA KGELTRAVTV EVSGASATAI AAVEKAGGSV KVAAKAEAPA E A

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Macromolecule #21: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 13.324717 KDa
SequenceString:
MIHPETNLEV ADNSGARQVQ CIKVLGGSKR KTASVGDVIV VSVKEAIPRG KVKKGDVHQA VIVRTSYPVR RADGSAIRFD KNAAVLINK SMEPIGTRIF GPVVRELRAR KFMKIISLAP EVL

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Macromolecule #22: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 17.559434 KDa
SequenceString:
MKTTLSLKPA EVTKGWTLID AEGLVLGRLA TIIATRLRGK HKPQYTPHVD CGDNIVVINA EKIVLTGNKV GQKLFHYHTG HPGGIKERT ITQRLEGKNP GSVIEKAVER MITRGPLQRA QMKHLYVYAG DKHPHEGQQP VKLDVASMNR KNTLNVIEA

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Macromolecule #23: Large ribosomal subunit protein bL9

MacromoleculeName: Large ribosomal subunit protein bL9 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 21.11975 KDa
SequenceString: MSQTEVILLQ RVEHLGQMGE IVRVKPGYAR NFLLPQGKAL RANAQNRQRF ETERAQLEAQ NLKRREEAER LAERMHGLSV VIIRQAGDS GSLYGSVTTR DIALAVTASG LTVGRNQVVL VEPIKMLGLV EARVDLHPEV SIPVTVNVAR SEEEAERQAR G EAVVAEED ...String:
MSQTEVILLQ RVEHLGQMGE IVRVKPGYAR NFLLPQGKAL RANAQNRQRF ETERAQLEAQ NLKRREEAER LAERMHGLSV VIIRQAGDS GSLYGSVTTR DIALAVTASG LTVGRNQVVL VEPIKMLGLV EARVDLHPEV SIPVTVNVAR SEEEAERQAR G EAVVAEED EYVLETEVEG DESAIEGEVE GAAV

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Macromolecule #24: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 19.490539 KDa
SequenceString:
MSRVGKYPVV IPAGVDISIT DGSLTAKGKR GSLTMPLTRF VEAKVEDGKV AILPVGNRSR ETWTMWGTTR AIVANLVKGV SEGFSKTLE ITGTGFRASV QGSNLVMNLG YSHDVVYPIP ADVKITTPRP TAITVEGNDK QRVGQVALDI RNFRKPEPYK G KGVRYETE VLRRKEGKKK

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Macromolecule #25: Large ribosomal subunit protein uL4

MacromoleculeName: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 21.74216 KDa
SequenceString: MEYDIKTLDN GSAGTVSLPE ELFGATPRAD IMARVVHWQL AKRRAGTHRT KGMGEVSGTT KKPFRQKGTG SARQGSLRAP QFRTGGVVH GPVVRDHGYD LPKKVRRLGL ISALSQKAAA GKLIVIDQAA GVTKTREAAA KLAALGWSSA LIVDGAVDVA F GRAVRNLP ...String:
MEYDIKTLDN GSAGTVSLPE ELFGATPRAD IMARVVHWQL AKRRAGTHRT KGMGEVSGTT KKPFRQKGTG SARQGSLRAP QFRTGGVVH GPVVRDHGYD LPKKVRRLGL ISALSQKAAA GKLIVIDQAA GVTKTREAAA KLAALGWSSA LIVDGAVDVA F GRAVRNLP KIDVLPTIGA NVYDILNHDV LVLTRAGLEG LKERLA

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Macromolecule #26: Large ribosomal subunit protein uL3

MacromoleculeName: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 24.438312 KDa
SequenceString: MRTGLIAKKL GMTRLFKEDG THVPVTVLHL DEVEVVDART QERDGYTAVQ IGMSKAKVKN VTKPMRGHYA RTKVEPKKTL VEFRVAEDA VLEAGTKLSA AHFVVGQKID VTGTSKGKGF AGVMKRWNFA GLEASHGVSI SHRSHGSTGQ RQDPGKVFKG K KMAGHMGD ...String:
MRTGLIAKKL GMTRLFKEDG THVPVTVLHL DEVEVVDART QERDGYTAVQ IGMSKAKVKN VTKPMRGHYA RTKVEPKKTL VEFRVAEDA VLEAGTKLSA AHFVVGQKID VTGTSKGKGF AGVMKRWNFA GLEASHGVSI SHRSHGSTGQ RQDPGKVFKG K KMAGHMGD ERITTLNLEV AAVDAERNLI MVRGSIPGAK DGLVMIRDAI KKARHADAPY PAATAAAAG

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Macromolecule #29: Large ribosomal subunit protein bL19

MacromoleculeName: Large ribosomal subunit protein bL19 / type: protein_or_peptide / ID: 29 / Details: Modelled from the close relative Asaia bogorensis / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 14.342386 KDa
SequenceString:
MNIVQQYEAR EIERLTAARP VPEFQAGDTV RVGVRVVEGT REERVQAYEG VVIARSNKGL NSNFTVRKIS NGEGVERIFP LYSPSIAEI AVVRRGKVRR AKLYYLRERS GKSARIAERP RDVAKTAS

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Macromolecule #30: Ribosome silencing factor S

MacromoleculeName: Ribosome silencing factor S / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 16.392545 KDa
SequenceString:
MKTAGTPRKK AAAAGPRKTR AAAAPRETVG RELVEKALGV ITTSLDEDKA EDIVTLDLRG RASFADHMVI ATGIADRQIA AMASHVEDK LNEIGIKRIT IEGANGTDWV LLDTGDIVVH LFKPESRALY ALERMWGKDL DDSAADEADT TDL

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Macromolecule #3: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 883.724 KDa
SequenceString: GAGAAGGGCA UUCGGUGGAU GCCUUGGCAU CAGGAGGCGA CGAAAGACGU GGCACGCUGC GAAAAGCCAC GGGGAGCUGC GAGCAAGCU UUGAUCCGUG GAUAUCUGAA UGGGGAAACC CACCUAGCGA UAGGUAUCAU GCCCUGAAUA CAUAGGGGUA U GAGGCGAA ...String:
GAGAAGGGCA UUCGGUGGAU GCCUUGGCAU CAGGAGGCGA CGAAAGACGU GGCACGCUGC GAAAAGCCAC GGGGAGCUGC GAGCAAGCU UUGAUCCGUG GAUAUCUGAA UGGGGAAACC CACCUAGCGA UAGGUAUCAU GCCCUGAAUA CAUAGGGGUA U GAGGCGAA CCCGGGGAAC UGAAACAUCU CAGUACCUGG AGGAAAAGAC AUCAACAGAG AUUCCGCUAG UAGUGGCGAG CG AACGCGG AACAGGCCAG UGGCCAUUGU GAAAGAAGCA GAACGGUCUG GAAAGUCCGG CGAUAAUGGG UGAUAGCCCC GUA UGCGUA GUGUUCACGA UGGUUCUUGA GUAGGGCGGG GCACGUGAAA CCCUGUCUGA ACAUGGGGGG ACCACCCUCC AAGC CUAAA UACUCCCUGA UGACCGAUAG UGAACAAGUA CCGUGAGGGA AAGGUGAAAA GCACCCCGAU GAGGGGAGUG AAAGA GACC UGAAACCGGA UGCCUACAAG CAGUCGGAGC CUCUUAUGGG GUGACGGCGU ACCUUUUGUA UAAUGGGUCA GCGAGU UUC UGUUUGCAGC GAGCUUAAGC CGGUAGGUGU AGGCGUAGCG AAAGCGAGUC UGAAUAGGGC GAAUGAGUUG CUGGCAG AA GACCCGAAAC CGAGUGAUCU AGCCAUGGCC AGGCUGAAGG UGCGGUAACA CGCACUGGAG GGCCGAACCC ACGCCUGU U GAAAAAGUCG GGGAUGAGCU GUGGCUAGGG GUGAAAGGCC AAUCAAACUC GGAGAUAGCU GGUUCUCCGC GAAAUCUAU UGAGGUAGAU CGUCACGUAU UGCCCUCGGG GGUAGAGCAC UGGAUGGGCU AGGGGGACCC AAAGUCUUAC CAAACCUAAC CAAACUCCG AAUACCGAGG AGUAUGAGCG UGGCAGACAG ACAGUGGGUG CUAAGGUCCA UUGUCGAGAG GGAAACAGCC C AGACCACC AGCUAAGGCC CCCAAAUCGU GGCUAAGUGG GAAAGGAUGU GGGGAUUCCA AAACAACCAG GAGGUUGGCU UA GAAGCAG CCAUCCUUUA AAGAAAGCGU AAUAGCUCAC UGGUCUAAUA GAAACCCUGC GCCGAAAAUG UAACGGGGCU CAA GCCACG UGCCGAAGCU GUGGGUGCAU AUCUUUGAUA UGCGCGGUAG CGGAGCGUUC CGUAGGUCUG CGAAGGAGAC GGGG UGACC CUCUCUGGAG AUAUCGGAAG UGCGAAUGCU GACAUGAGUA GCGACAAACA GUGCGAGAAA CACUGUCGCC GAAAG UCCA AGGGUUCCUG CGCAAGGUUA AUCCACGCAG GGUGAGCCGG CCCCUAAGGC GAGGGCGAAA GCCGUAGUCG AUGGGA ACC AGUUGAAUAU UACUGGGCCU GCCAGAAGUG ACGAAUGCAA UAUGUUGUCU GGUCUUAUUG GAUUGACCAG GCUUUUG GA GCAUUCCAGG AAAUAGCUCU GGCGUAUAGA CCGUACCCGA AACCGACACA GGUGGACUGG UAGAGAAUAC CAAGGCGC U UGAGAGAACG AUGCUGAAGG AACUAGGCAA AUUACUUGUG UAACUUCGGG AUAAGCAAGA CCCGUAUGUG GGCAACCAU GUGCGGGUGG CACAGACCAG GGGGUAGCGA CUGUUUAGUA AAAACACAGG GCUGUGCGAA GUCGAGAGAC GACGUAUACG GCCUGACGC CUGCCCGGUG CCGGAAGGUU AAGAGGAGAU GUGCAAGCAU UGAAUUGAAG CCCCGGUAAA CGGCGGCCGU A ACUAUAAC GGUCCUAAGG UAGCGAAAUU CCUUGUCGGG UAAGUUCCGA CCUGCACGAA UGGCGUAACG ACUUCCCCAC UG UCUCCAG CAUCGACUCA GCGAAAUUGA AUUCCCCGUG AAGAUGCGGG GUACCCGCGG UCAGACGGAA AGACCCUAUG AAC CUUUAC UGCAGCUUUG CAGUGGCAUC AGAGACAUCC UGUGUAGGAU AGGUGGGAGG CUAUGAACCC GAGGCGCCAG CUUC GGUGG AGCCGUCCUU GAAAUACCAC CCUGAAUUUU UCUGAUGUCU AACCGAGACC AGUCUAGCCU GGUCCGGGAC CCUGC AUGG UGGGCAGUUU GACUGGGGCG GUCGCCUCCC AAAGUGUAAC GGAGGCGCGC GAUGGUGGGC UCAGGUCGGU CGGAAA CCG ACUGUCGAGU GCAAUGGCAU AAGCCCGCCU GACUGUGAGA GUGACAGCUC GAACAGAGAC GAAAGUCGGC CAUAGUG AU CCGGUGGUCC CACGUGGACG GGCCAUCGCU CAACGGAUAA AAGGUACUCU AGGGAUAACA GGCUGAUCUC CCCCAAGA G UCCACAUCGA CGGGGAGGUU UGGCACCUCG AUGUCGGCUC AUCACAUCCU GGGGCUGGAG CAGGUCCCAA GGGUUCGGC UGUUCGCCGA UUAAAGUGGU ACGUGAGCUG GGUUUAGAAC GUCGUGAGAC AGUUCGGUCC CUAUCUGCCG UGGGUGUAUG AGACUUGAG AGGAUUUGUC CCUAGUACGA GAGGACCGGG AUGAACAUAC CUCUGGUGUA CCGGUUGUCG CGCCAGCGGC A CAGCCGGG UAGCUAAGUA UGGACGGGAU AACCGCUGAA AGCAUCUAAG CGGGAAACCC ACCUCAAAAC UAGGUCUCAC AG GGCCGUG AAAGACCAUC ACGUCAAUAG GCCGGGUGUG GAAGCGUGGU AACACGUGAA GCUAACCGGU CCUAAUCGCC CAU AUCGCU

GENBANK: GENBANK: AP043925.1

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Macromolecule #27: E-site tRNA (heterogeneous fragment modelled as poly-U with the C...

MacromoleculeName: E-site tRNA (heterogeneous fragment modelled as poly-U with the CCA-end)
type: rna / ID: 27 / Number of copies: 1
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 5.487099 KDa
SequenceString:
UUUUUUUUUU UUUUUCCA

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Macromolecule #28: 5S rRNA (fragment)

MacromoleculeName: 5S rRNA (fragment) / type: rna / ID: 28 / Number of copies: 1
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Molecular weightTheoretical: 36.341637 KDa
SequenceString:
CUGGUGGCUA UGGCGGGAGA CUUCCACCCG AUCCCAUCCC GAACUCGGAC GUGAAACGCC CCAGCGCCUA UGAUACUGCA UCUUAAGAU GCGGAAAAGU CGGUCGCCGC CAGG

GENBANK: GENBANK: AP043925.1

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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

Concentration0.642 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris hydrochloride
20.0 mMMg(CH3COO)2Magnesium acetate
50.0 KClKClPotassium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.0)
Software - details: cryoSPARC was used to process cryo-EM data
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0)
Software - details: cryoSPARC was used to process cryo-EM data
Number images used: 48969
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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