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- EMDB-42577: Cryo-EM structure of the Listeria innocua 50S ribosomal subunit i... -

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Basic information

Entry
Database: EMDB / ID: EMD-42577
TitleCryo-EM structure of the Listeria innocua 50S ribosomal subunit in complex with HflXr (structure III)
Map dataCryo-EM map of the Listeria innocua 50S ribosomal subunit in complex with HflXr (structure III)
Sample
  • Complex: Listeria innocua 50S ribosomal subunit bound to HflXr
    • Protein or peptide: x 27 types
    • RNA: x 2 types
  • Protein or peptide: x 1 types
  • Ligand: x 5 types
Keywordscryo-EM / recycling / HflXr / time-resolved / RIBOSOME
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site ...Ribosomal protein L31 type B / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L30, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30 signature. / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L29 signature. / Ribosomal protein L5 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / ribosomal L5P family C-terminus / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L16p/L10e
Similarity search - Domain/homology
Large ribosomal subunit protein bL31B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL21 ...Large ribosomal subunit protein bL31B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL19
Similarity search - Component
Biological speciesListeria innocua (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSeely SM / Basu RS / Gagnon MG
Funding support United States, 4 items
OrganizationGrant numberCountry
Other governmentUniversity of Texas Medical Branch
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136936 United States
Welch FoundationH-2032-20230405 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008280 United States
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Mechanistic insights into the alternative ribosome recycling by HflXr.
Authors: Savannah M Seely / Ritwika S Basu / Matthieu G Gagnon /
Abstract: During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue ...During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom.
History
DepositionOct 31, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42577.png

Downloads & links

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Map

FileDownload / File: emd_42577.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the Listeria innocua 50S ribosomal subunit in complex with HflXr (structure III)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.7117576 - 2.373201
Average (Standard dev.)-0.0018904322 (±0.08374061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42577_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Listeria innocua 50S ribosomal subunit in complex with...

Fileemd_42577_additional_1.map
AnnotationListeria innocua 50S ribosomal subunit in complex with HflXr (structure III) Sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Listeria innocua 50S ribosomal subunit in complex with...

Fileemd_42577_half_map_1.map
AnnotationListeria innocua 50S ribosomal subunit in complex with HflXr (structure III) Half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Listeria innocua 50S ribosomal subunit in complex with...

Fileemd_42577_half_map_2.map
AnnotationListeria innocua 50S ribosomal subunit in complex with HflXr (structure III) Half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Listeria innocua 50S ribosomal subunit bound to HflXr

EntireName: Listeria innocua 50S ribosomal subunit bound to HflXr
Components
  • Complex: Listeria innocua 50S ribosomal subunit bound to HflXr
    • Protein or peptide: GTPase HflXr
    • RNA: 23S Ribosomal RNA
    • RNA: 5S Ribosomal RNA
    • Protein or peptide: Large ribosomal subunit protein uL2
    • Protein or peptide: Large ribosomal subunit protein uL3
    • Protein or peptide: Large ribosomal subunit protein uL4
    • Protein or peptide: Large ribosomal subunit protein uL5
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: Large ribosomal subunit protein uL13
    • Protein or peptide: Large ribosomal subunit protein uL14
    • Protein or peptide: Large ribosomal subunit protein uL15
    • Protein or peptide: Large ribosomal subunit protein uL16
    • Protein or peptide: Large ribosomal subunit protein bL17
    • Protein or peptide: Large ribosomal subunit protein uL18
    • Protein or peptide: Large ribosomal subunit protein bL19
    • Protein or peptide: Large ribosomal subunit protein bL20
    • Protein or peptide: Large ribosomal subunit protein bL21
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: Large ribosomal subunit protein bL27
    • Protein or peptide: Large ribosomal subunit protein bL28
    • Protein or peptide: Large ribosomal subunit protein uL29
    • Protein or peptide: Large ribosomal subunit protein uL30
    • Protein or peptide: Large ribosomal subunit protein bL31B
    • Protein or peptide: Large ribosomal subunit protein bL32
    • Protein or peptide: Large ribosomal subunit protein bL33
    • Protein or peptide: Large ribosomal subunit protein bL34
    • Protein or peptide: Large ribosomal subunit protein bL35
    • Protein or peptide: Large ribosomal subunit protein bL36
  • Protein or peptide: Large ribosomal subunit protein uL24
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM IONPotassium
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Listeria innocua 50S ribosomal subunit bound to HflXr

SupramoleculeName: Listeria innocua 50S ribosomal subunit bound to HflXr / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19, #21-#30
Source (natural)Organism: Listeria innocua (bacteria)
Molecular weightTheoretical: 1.5 MDa

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Macromolecule #1: GTPase HflXr

MacromoleculeName: GTPase HflXr / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 47.61093 KDa
SequenceString: MEKKVLIVGI SQKQKDFDYS MEELANLAAA NNMEVVGEIR QNIDRENRAT YVGKGKVDEI KGLAEMQDAR LIIFNDELSP SQIRNLEEA LELDVMDRTG LILAIFANRA KTKEAQLQVQ IAKLQYELPR IFGQGEDMDQ QSGKGGLSNR GSGEKKIETD R RTIKHQIR ...String:
MEKKVLIVGI SQKQKDFDYS MEELANLAAA NNMEVVGEIR QNIDRENRAT YVGKGKVDEI KGLAEMQDAR LIIFNDELSP SQIRNLEEA LELDVMDRTG LILAIFANRA KTKEAQLQVQ IAKLQYELPR IFGQGEDMDQ QSGKGGLSNR GSGEKKIETD R RTIKHQIR HLQKELDMLV DDREVRRRKR KKNEIPVVSL VGYTNAGKST TMNGLVRAYS ETADKQVFEK DMLFATLETS VR EIVLPDN KQFLLTDTVG FVSKLPHQLV KAFRSTLEEA RDADLLIHVV DYSDPHYKTM MKTTEETLKV VGVEDVPVIY AYN KADLLE DEMYPKQTGN TIIFSAREEE SLEFLTEVIR KELFASYEKA TFLIPFEAGQ VVAYLNEHAD ILETEYLENG TQIV AEVSP ADLQKLAEYQ VAE

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Macromolecule #4: Large ribosomal subunit protein uL2

MacromoleculeName: Large ribosomal subunit protein uL2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 30.568367 KDa
SequenceString: MAIKKYKPTT NGRRHMTSSD FAEITTSTPE KSLLRPLKKK AGRNNQGKLT VRHHGGGHKR QYRVIDFKRN KDGIPGRVAT IEYDPNRSA NIALINYADG EKRYIIAAKG LEVGQTIYSG AEADIKVGNA LELKDIPVGT VIHNIEMKPG KGGQLVRSAG T SAQVLGKE ...String:
MAIKKYKPTT NGRRHMTSSD FAEITTSTPE KSLLRPLKKK AGRNNQGKLT VRHHGGGHKR QYRVIDFKRN KDGIPGRVAT IEYDPNRSA NIALINYADG EKRYIIAAKG LEVGQTIYSG AEADIKVGNA LELKDIPVGT VIHNIEMKPG KGGQLVRSAG T SAQVLGKE GKYVLIRLNS GEVRMILATC RATIGQVGNE QHELINIGKA GRSRWMGKRP TVRGSVMNPN DHPHGGGEGK AP IGRKSPM SPWGKPTLGY KTRKKNNNSD KFIVRRRKKK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #5: Large ribosomal subunit protein uL3

MacromoleculeName: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 22.880467 KDa
SequenceString: MTKGILGRKV GMTQVFTENG ELIPVTVIEA AQNVVLQKKT VETDGYEAVQ IGFEDKRAKL SNKPEQGHVA KADTTPKRFI REFRDVNLD EYEIGAEVKV DVFAEGDIID ATGVSKGKGF QGVIKRHGQS RGPMAHGSRY HRRPGSMGPV APNRVFKNKL L PGRMGGEQ ...String:
MTKGILGRKV GMTQVFTENG ELIPVTVIEA AQNVVLQKKT VETDGYEAVQ IGFEDKRAKL SNKPEQGHVA KADTTPKRFI REFRDVNLD EYEIGAEVKV DVFAEGDIID ATGVSKGKGF QGVIKRHGQS RGPMAHGSRY HRRPGSMGPV APNRVFKNKL L PGRMGGEQ ITIQNLEIVK VDVEKNVLLV KGNVPGAKKA LVQIKTATKA K

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #6: Large ribosomal subunit protein uL4

MacromoleculeName: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 22.640262 KDa
SequenceString: MPKLSLLKQD GTNAGEITLN DTVFGIEPNE KVVVDVILSQ RASLRQGTHK VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVV FGPTPRSYAY KLPKKVRRLA IKSILSSKVN EEKLVVLEGL TFDAPKTKEF AAFLKNISVD TKALIVVAGE S ENVELSAR ...String:
MPKLSLLKQD GTNAGEITLN DTVFGIEPNE KVVVDVILSQ RASLRQGTHK VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVV FGPTPRSYAY KLPKKVRRLA IKSILSSKVN EEKLVVLEGL TFDAPKTKEF AAFLKNISVD TKALIVVAGE S ENVELSAR NLQGITVIPA ESISVLEVAK HDKLIITKAA VEKVEEVLA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #7: Large ribosomal subunit protein uL5

MacromoleculeName: Large ribosomal subunit protein uL5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 20.023248 KDa
SequenceString:
MNRLKDQYLK EIVPALMSKF NYDSVMEVPK IDKIVINTGV GDATANAKVL DSAVEELALI TGQKPVITKA KNSIAGFRLR EGMPIGAKV TLRGERMYDF LDKLVTVSLP RVRDFRGVSK KAFDGRGNYT LGVREQLIFP EIDYDQVSKV RGMDVVIVTT A KSDEESHE LLTQLGMPFQ K

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #8: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 19.433316 KDa
SequenceString:
MSRIGKKTIV IPAGVTVTLN GSTATVKGPK GELVKEFNPE ITINIEGNEI NVSRPTDNKN HRALHGTTRA ILNNMVVGVS EGYEKKLEL IGVGYRAQKQ GDKLVLNVGY SHPVEFVAPK GVEIEVPANT QVIVKGYNKE HVGELAANIR AVRPPEPYKG K GIRYEGEH VRRKEGKTGK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #9: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 16.228722 KDa
SequenceString:
MRTTYMAKPG EVERKWYVID ATGVSLGRLS SEVASILRGK NKPQFTPHID TGDFVIIINA GKIGLTGKKA TDKIYYRHSQ YPGGLKSRT AGEMRTNNPE KLLELSIKGM LPKNSLGRQL FKKLHVYGGS EHEHAAQKPE VYELRG

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #10: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 13.248427 KDa
SequenceString:
MIQQESRMKV ADNSGAREVL TIKVLGGSGR KTANIGDVVV CTVKQATPGG VVKKGEVVKA VIVRTKSGAR RQDGSYIKFD ENACVIIRD DKSPRGTRIF GPVARELREN NFMKIVSLAP EVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #11: Large ribosomal subunit protein uL15

MacromoleculeName: Large ribosomal subunit protein uL15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 15.827128 KDa
SequenceString:
MKLHELKPSE GSRKERNRVG RGTGSGNGKT SGRGHKGQKA RSGGGVRLGF EGGQLPLFRR IPKRGFTNIN RKEFAIVNLD VLNRFEDGT EVTPELLIET GIIRNEKSGI KILSDGNIEK KLTVKANKFS AAAKEAIEAA GGKTEVI

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #12: Large ribosomal subunit protein uL16

MacromoleculeName: Large ribosomal subunit protein uL16 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 16.171043 KDa
SequenceString:
MLVPKRVKYR REFRGNMRGR AKGGTEVAFG EYGLQAVEAS WITNRQIEAA RIAMTRYMKR GGKVWIKIFP HKSYTSKPIG VRMGKGKGA PEGWVSPVKR GKIMFEIAGV PEDVAREALR LAAHKLPVKT KIVKREEIGG EANES

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #13: Large ribosomal subunit protein bL17

MacromoleculeName: Large ribosomal subunit protein bL17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 15.237766 KDa
SequenceString:
MGYRKLGRTS SQRKALLRDL ATDLIVHERI ETTEARAKEI RKVVEKLITS GKKGDLHARR QAAAFIRHEV VEVVQVDAKG KDGSTVKKN RPVYALQKLF DDVAPRYAER QGGYTRILKK GPRRGDGAPM VIIELV

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #14: Large ribosomal subunit protein uL18

MacromoleculeName: Large ribosomal subunit protein uL18 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 13.107909 KDa
SequenceString:
MITKIDKNKV RKKRHARVRS KISGTESRPR LNVFRSNKNI YAQVIDDVNG VTLASASNLD KDFGSAESKV DAASKVGELV AKRASEKGI TSVTFDRGGY LYHGRVKALA EAARENGLEF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #15: Large ribosomal subunit protein bL19

MacromoleculeName: Large ribosomal subunit protein bL19 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 13.089413 KDa
SequenceString:
MNKLIDEITK SQLNPDVPSF RPGDTVRVHA KVVEGTRERI QLFEGVVIKR RGAGISETFT VRKISNGVGV ERTFPVHTPR IAKLEVIRR GKVRRAKLYY LRNLRGKAAR IKEIR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #16: Large ribosomal subunit protein bL20

MacromoleculeName: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 13.71935 KDa
SequenceString:
MPRVKGGTVT RKRRKKIVKL AKGYYGSKHL LFKVANQAVM KSYQYAYRDR RQKKRDFRRL WIARINAAAR MQDLSYSKLM HGLKLAGID INRKMLADLA VNDIASFNTL ADSAKKALAK

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #17: Large ribosomal subunit protein bL21

MacromoleculeName: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 11.220003 KDa
SequenceString:
MYAIIETGGK QIKVEAGQEI YVEKLAGEVG DVVTFDKVLF VGGDSAKVGV PFVDGATVTA KVEKQGRAKK LTVYKYKPKK NYHKKQGHR QPYTKLTIDA INA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #18: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 12.895945 KDa
SequenceString:
MASEVTSAKA VAKTVRIAPR KARIVIDLIR GKQVGEAIAI LKYTPRSASP IIEKVLKSAI ANAEHNYDLD INNLVVEEAF VDEGPTLKR FRPRAQGRAS AINKRTSHIT VVVSEVKEG

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #19: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 10.949682 KDa
SequenceString:
MDARDIIKRP VVTEESTSIL DDKKYTFEVD TRATKTQVKY AIEEIFDVKV AKVNVMNYKG KLKRMGRYAG YTNKRRKAIV TVTADSKEI QFFEV

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #20: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 11.21933 KDa
SequenceString:
MHVKKGDKVK VITGKDKGKS GKVLAAFPKK DRVLIEGINM VKKHTKPSNI NPQGGILNVE APIHVSNVML IDPKTGEPTR VGYEVKGDK KVRVAKKSGE VIDK

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #21: Large ribosomal subunit protein bL27

MacromoleculeName: Large ribosomal subunit protein bL27 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 10.57193 KDa
SequenceString:
MLKFDIQHFA HKKGGGSTSN GRDSESKRLG AKRADGQFVT GGSILYRQRG TKIYPGTNVG RGGDDTLFAK TDGVVRFERM GRDKKKVSV YPEVQEA

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #22: Large ribosomal subunit protein bL28

MacromoleculeName: Large ribosomal subunit protein bL28 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 7.010383 KDa
SequenceString:
MAKECVITGR KSRSGNKRSH AMNSSKRTWK ANLQKVRILV NGKPKKVWVS ARALKSGKVE RV

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #23: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 7.414548 KDa
SequenceString:
MKANDIRDLS TTEIQDQEKA LKEELFNLRF QLATGQLENT ARIREVRKAI ARMKTIVRER ELA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #24: Large ribosomal subunit protein uL30

MacromoleculeName: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 6.504753 KDa
SequenceString:
MAKLEITLKR SLIGRPQPQR KTVQALGLGK TNSVVVKEDN PAIRGMITKV SHLVDVKEV

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #25: Large ribosomal subunit protein bL31B

MacromoleculeName: Large ribosomal subunit protein bL31B / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 9.27436 KDa
SequenceString:
MKTGIHPEYR PVVFVDTSTD FKFLSGSTKS SSETIKWEDG NEYPLLRVEI SSDSHPFYTG KQKHATADGR VDRFNKKYGL K

UniProtKB: Large ribosomal subunit protein bL31B

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Macromolecule #26: Large ribosomal subunit protein bL32

MacromoleculeName: Large ribosomal subunit protein bL32 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 6.534564 KDa
SequenceString:
MAVPFRRTSK AKKRKRRTHV KLQLPGMNEC SNCGEYRLSH HVCPECGQYD GKDVANS

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #27: Large ribosomal subunit protein bL33

MacromoleculeName: Large ribosomal subunit protein bL33 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 6.021034 KDa
SequenceString:
MRVNITLECT ECGDRNYITT KNKRENPERI ELKKYCPRLR RVTLHRETK

UniProtKB: Large ribosomal subunit protein bL33

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Macromolecule #28: Large ribosomal subunit protein bL34

MacromoleculeName: Large ribosomal subunit protein bL34 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 5.319457 KDa
SequenceString:
MKRTYQPSKR KRKKVHGFRT RMSTKNGRRV LASRRRKGRK VLSA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #29: Large ribosomal subunit protein bL35

MacromoleculeName: Large ribosomal subunit protein bL35 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 7.746438 KDa
SequenceString:
MPKMKTHRGS AKRFKRTGSG KLKRRHGFTS HMFANKSQKQ KRKLRKSAMV SAGDFKRIRQ MVAKMK

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #30: Large ribosomal subunit protein bL36

MacromoleculeName: Large ribosomal subunit protein bL36 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 4.33646 KDa
SequenceString:
MKVRPSVKPM CEKCKVIRRK GKVMVICENP KHKQKQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #2: 23S Ribosomal RNA

MacromoleculeName: 23S Ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 951.06175 KDa
SequenceString: GGUUAAGUUA GAAAGGGCGC ACGGUGGAUG CCUUGGCACU AGGAGCCGAA GAAGGACGGG ACUAACACCG AUAUGCUUUG GGGAGCUGU ACGUAAGCGU UGAUCCAGAG AUUUCCGAAU GGGGGAACCC ACUAUCUUUA GUCGGAUAGU AUCCUUACGU G AAUACAUA ...String:
GGUUAAGUUA GAAAGGGCGC ACGGUGGAUG CCUUGGCACU AGGAGCCGAA GAAGGACGGG ACUAACACCG AUAUGCUUUG GGGAGCUGU ACGUAAGCGU UGAUCCAGAG AUUUCCGAAU GGGGGAACCC ACUAUCUUUA GUCGGAUAGU AUCCUUACGU G AAUACAUA GCGUGAGGAA GGCAGACCCA GGGAACUGAA ACAUCUAAGU ACCUGGAGGA AGAGAAAGAA AAAUCGAUUU CC UGAGUAG CGGCGAGCGA AACGGAAAGA GCCCAAACCA AGAAGCUUGC UUCUUGGGGU UGUAGGACAC UCUAUACGGA GUU ACAAAA GAAAGUUAUA AAUGAAGCGG UCUGGAAAGG CCCGCCAAAG ACGGUAACAG CCCGGUAGUU GAAAUGGCUU UCCC UCCAG AGUGGAUCCU GAGUACGACG GAACACGUGA AAUUCCGUCG GAAUCCGGGA GGACCAUCUC CCAAGGCUAA AUACU CCCU AGUGACCGAU AGUGAACCAG UACCGUGAGG GAAAGGUGAA AAGCACCCCG GAAGGGGAGU GAAACAGUUC CUGAAA CCG UGUGCCUACA AGUAGUUAGA GCCCGUUAAU GGGUGAUAGC GUGCCUUUUG UAGAAUGAAC CGGCGAGUUA CGAUUUG UU GCAAGGUUAA GCGGAAAAAG CGGAGCCGUA GCGAAAGCGA GUCUGAAUAG GGCGCAUAAG UAACAGGUCG UAGACCCG A AACCAGGUGA UCUACCCAUG UCCAGGAUGA AGGUAAGGUA AUACUUACUG GAGGUCCGAA CCCACGCACG UUGAAAAGU GCGGGGAUGA GGUGUGGGUA GCGGAGAAAU UCCAAUCGAA CUUGGAGAUA GCUGGUUCUC UCCGAAAUAG CUUUAGGGCU AGCCUCGAG GUAAAGAGUC AUGGAGGUAG AGCACUGUUU GGACUAGGGG CCCUUCUCGG GUUACCGAAU UCAGAUAAAC U CCGAAUGC CAUGUACUUA UACUCGGGAG UCAGACUGCG AGUGAUAAGA UCCGUAGUCG AAAGGGAAAC AGCCCAGACC AC CAGUUAA GGUCCCCAAA UAUAUGUUAA GUGGAAAAGG AUGUGGGGUU GCUUAGACAA CCAGGAUGUU GGCUUAGAAG CAG CCACCA UUGAAAGAGU GCGUAAUAGC UCACUGGUCG AGUGACCCCG CGCCGAAAAU GUACCGGGGC UAAACAUAUU ACCG AAACU GUGGAUGAAC CUCUUCGGAG GUUCGUGGUA GGAGAGCGUU CUAAGGGCGG UGAAGUCAGA CCGGAAGGAC UGGUG GAGC GCUUAGAAGU GAGAAUGCCG GUAUGAGUAG CGAAAGAAGG GUGAGAAUCC CUUCCACCGA AUAUCUAAGG UUUCCU GAG GAAGGCUCGU CCGCUCAGGG UUAGUCGGGA CCUAAGCCGA GGCCGAUAGG CGUAGGCGAU GGACAACAGG UAGAGAU UC CUGUACCAGU GCUAAUUGUU UAACCGAUGG GGUGACACAG AAGGAUAGGG AAUCGCACGA AUGGAAAUGU GCGUCCAA G CAGUGAGUGU GAGAAGUAGG CAAAUCCGCU UCUUGCGAAG CAUGAGCUGU GAUGGGGAAG GAAAUUAAGU ACGGAAGUU CCUGAUUUCA CGCUGUCAAG AAAAGCCUCU AGGAAGAGUA GUACUGCCCG UACCGCAAAC CGACACAGGU AGAUGAGGAG AGAAUCCUA AGGUGAGCGA GAGAACUCUC GUUAAGGAAC UCGGCAAAAU GACCCCGUAA CUUCGGGAGA AGGGGUGCUC U AUUAGGGU GCAAGCCCGA GAGAGCCGCA GUGAAUAGGC CCAGGCGACU GUUUAGCAAA AACACAGGUC UCUGCAAAAC CG UAAGGUG ACGUAUAGGG GCUGACGCCU GCCCGGUGCU GGAAGGUUAA GAGGAGUGCU UAGCUUCGGC GAAGGUACGA AUU GAAGCC CCAGUAAACG GCGGCCGUAA CUAUAACGGU CCUAAGGUAG CGAAAUUCCU UGUCGGGUAA GUUCCGACCC GCAC GAAAG GCGCAACGAU CUGGGCACUG UCUCAACGAG AGACUCGGUG AAAUUAUAGU ACCUGUGAAG AUGCAGGUUA CCCGC GACA GGACGGAAAG ACCCCGUGGA GCUUUACUGC AACCUGAUAU GGAAUGUUUG UACCGCUUGU ACAGGAUAGG UAGGAG CCG AAGAGACGUG UGCGCUAGCA UACGAGGAGG CAAUGGUGGG AUACUACCCU GGCUGUAUGA CCAUUCUAAC CCGCCAC GC UAAGCGCGUG GGGAGACAGU GUCAGGUGGG CAGUUUGACU GGGGCGGUCG CCUCCUAAAG AGUAACGGAG GCGCCCAA A GGUUCCCUCA GAAUGGAUGG AAAUCAUUCG CAGAGUGUAA AGGCACAAGG GAGCUUGACU GCGAGACUGA CAAGUCGAG CAGGGACGAA AGUCGGGCUU AGUGAUCCGG UGGUUCCGCA UGGAAGGGCC AUCGCUCAAC GGAUAAAAGC UACCCCGGGG AUAACAGGC UUAUCUCCCC CAAGAGUCCA CAUCGACGGG GAGGUUUGGC ACCUCGAUGU CGGCUCGUCG CAUCCUGGGG C UGUAGUCG GUCCCAAGGG UUGGGCUGUU CGCCCAUUAA AGCGGCACGC GAGCUGGGUU CAGAACGUCG UGAGACAGUU CG GUCCCUA UCCGUCGCGG GCGCAGGAAA UUUGAGAGGA GCUGUCCUUA GUACGAGAGG ACCGGGAUGG ACACACCGCU GGU GUACCA GUUGUUCCGC CAGGAGCAUC GCUGGGUAGC UAUGUGUGGC AGGGAUAAAC GCUGAAAGCA UCUAAGCGUG AAGC CCCCC UCAAGAUGAG AUUUCCCAUU UCUUCGGAAA GUAAGAUCCC UGAAAGAUGA UCAGGUAGAU AGGUUUGGAG UGGAA GUGU AGCGAUACAU GGAGCGGACA AAUACUAAUC GAUCGAGGAC UUAACCAA

GENBANK: GENBANK: CP102627.1

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Macromolecule #3: 5S Ribosomal RNA

MacromoleculeName: 5S Ribosomal RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Listeria innocua (bacteria) / Strain: ATCC33090
Molecular weightTheoretical: 37.304059 KDa
SequenceString:
UCUGGUAGUU AUGGCGAGAA GGUCACACCC GUUCCCAUCC CGAACACGGU AGUUAAGCUU CUCUGCGCCA AUGGUAGUUG GGGGCUUCC CCCUGCGAGA GUAGGUCGCU GCCGGGC

GENBANK: GENBANK: CP045743.1

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Macromolecule #31: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 31 / Number of copies: 1 / Formula: GCP
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #32: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 32 / Number of copies: 200 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #33: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #34: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 34 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #35: water

MacromoleculeName: water / type: ligand / ID: 35 / Number of copies: 134 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: 7.6
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 10446 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 332513

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Atomic model buiding 1

Initial modelPDB ID:

7nhn


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8uua:
Cryo-EM structure of the Listeria innocua 50S ribosomal subunit in complex with HflXr (structure III)

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