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- EMDB-15204: Cryo-EM structure of Listeria monocytogenes 50S ribosomal subunit. -

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Basic information

Entry
Database: EMDB / ID: EMD-15204
TitleCryo-EM structure of Listeria monocytogenes 50S ribosomal subunit.
Map dataPost-processed masked final volume
Sample
  • Complex: Listeria monocytogenes 50S ribosomal subunit.
    • Protein or peptide: x 27 types
    • RNA: x 2 types
  • Ligand: x 5 types
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome ...large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / 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 uL24 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 ...Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32B / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL30
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKoller TO / Crowe-McAuliffe C / Wilson DN
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Other governmentDLR01KI1820
Swedish Research Council2018-00956 Sweden
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes.
Authors: Timm O Koller / Kathryn J Turnbull / Karolis Vaitkevicius / Caillan Crowe-McAuliffe / Mohammad Roghanian / Ondřej Bulvas / Jose A Nakamoto / Tatsuaki Kurata / Christina Julius / Gemma C ...Authors: Timm O Koller / Kathryn J Turnbull / Karolis Vaitkevicius / Caillan Crowe-McAuliffe / Mohammad Roghanian / Ondřej Bulvas / Jose A Nakamoto / Tatsuaki Kurata / Christina Julius / Gemma C Atkinson / Jörgen Johansson / Vasili Hauryliuk / Daniel N Wilson /
Abstract: HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers ...HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers resistance to macrolide and lincosamide antibiotics by an experimentally unexplored mechanism. Here, we have determined cryo-EM structures of L. monocytogenes HflXr-50S and HflX-50S complexes as well as L. monocytogenes 70S ribosomes in the presence and absence of the lincosamide lincomycin. While the overall geometry of HflXr on the 50S subunit is similar to that of HflX, a loop within the N-terminal domain of HflXr, which is two amino acids longer than in HflX, reaches deeper into the peptidyltransferase center. Moreover, unlike HflX, the binding of HflXr induces conformational changes within adjacent rRNA nucleotides that would be incompatible with drug binding. These findings suggest that HflXr confers resistance using an allosteric ribosome protection mechanism, rather than by simply splitting and recycling antibiotic-stalled ribosomes.
History
DepositionJun 16, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15204.png

Downloads & links

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Map

FileDownload / File: emd_15204.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed masked final volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 420 pix.
= 344.4 Å		0.82 Å/pix.
x 420 pix.
= 344.4 Å		0.82 Å/pix.
x 420 pix.
= 344.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.091671824 - 0.22835511
Average (Standard dev.)0.0015240259 (±0.008589059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: final 3D refined volume

Fileemd_15204_additional_1.map
Annotationfinal 3D refined volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map1

Fileemd_15204_half_map_1.map
AnnotationHalf-map1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map2

Fileemd_15204_half_map_2.map
AnnotationHalf-map2
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Listeria monocytogenes 50S ribosomal subunit.

EntireName: Listeria monocytogenes 50S ribosomal subunit.
Components
  • Complex: Listeria monocytogenes 50S ribosomal subunit.
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L31 type BRibosome
    • Protein or peptide: 50S ribosomal protein L32-2Ribosome
    • Protein or peptide: 50S ribosomal protein L33 1Ribosome
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L27
  • Ligand: ZINC ION
  • Ligand: SPERMIDINE
  • Ligand: MAGNESIUM ION
  • Ligand: 1,4-DIAMINOBUTANEPutrescine
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: Listeria monocytogenes 50S ribosomal subunit.

SupramoleculeName: Listeria monocytogenes 50S ribosomal subunit. / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#29
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 7.010383 KDa
SequenceString:
MAKECVITGR KSRSGNKRSH AMNSSKRTWK ANLQKVRILV NGKPKKVWVS ARALKSGKVE RV

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Macromolecule #2: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 7.414548 KDa
SequenceString:
MKANDIRDLS TTEIQDQEKA LKEELFNLRF QLATGQLENT ARIREVRKAI ARMKTIVRER ELA

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Macromolecule #3: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 6.504753 KDa
SequenceString:
MAKLEITLKR SLIGRPQPQR KTVQALGLGK TNSVVVKEDN PAIRGMITKV SHLVDVKEV

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Macromolecule #4: 50S ribosomal protein L31 type B

MacromoleculeName: 50S ribosomal protein L31 type B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 9.27436 KDa
SequenceString:
MKTGIHPEYR PVVFVDTSTD FKFLSGSTKS SSETIKWEDG NEYPLLRVEI SSDSHPFYTG KQKHATADGR VDRFNKKYGL K

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Macromolecule #5: 50S ribosomal protein L32-2

MacromoleculeName: 50S ribosomal protein L32-2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 6.534564 KDa
SequenceString:
MAVPFRRTSK AKKRKRRTHV KLQLPGMNEC SNCGEYRLSH HVCPECGQYD GKDVANS

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Macromolecule #6: 50S ribosomal protein L33 1

MacromoleculeName: 50S ribosomal protein L33 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 6.021034 KDa
SequenceString:
MRVNITLECT ECGDRNYITT KNKRENPERI ELKKYCPRLR RVTLHRETK

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Macromolecule #7: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 5.319457 KDa
SequenceString:
MKRTYQPSKR KRKKVHGFRT RMSTKNGRRV LASRRRKGRK VLSA

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Macromolecule #8: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 7.746438 KDa
SequenceString:
MPKMKTHRGS AKRFKRTGSG KLKRRHGFTS HMFANKSQKQ KRKLRKSAMV SAGDFKRIRQ MVAKMK

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Macromolecule #9: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 4.33646 KDa
SequenceString:
MKVRPSVKPM CEKCKVIRRK GKVMVICENP KHKQKQG

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Macromolecule #12: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
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

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Macromolecule #13: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 22.863459 KDa
SequenceString: MTKGILGRKV GMTQVFTENG ELIPVTVIEA AQNVVLQKKT VETDGYEAVQ IGFEDKRAIL SNKPEQGHVA KANTTPKRFI REFRDVNLD EYEIGAEVKV DVFAEGDIID ATGVSKGKGF QGVIKRHGQS RGPMAHGSRY HRRPGSMGPV APNRVFKNKL L PGRMGGEQ ...String:
MTKGILGRKV GMTQVFTENG ELIPVTVIEA AQNVVLQKKT VETDGYEAVQ IGFEDKRAIL SNKPEQGHVA KANTTPKRFI REFRDVNLD EYEIGAEVKV DVFAEGDIID ATGVSKGKGF QGVIKRHGQS RGPMAHGSRY HRRPGSMGPV APNRVFKNKL L PGRMGGEQ ITIQNLEIVK VDVEKNVLLV KGNVPGAKKA LVQIKTATKA K

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Macromolecule #14: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
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

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Macromolecule #15: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
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

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Macromolecule #16: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 19.434365 KDa
SequenceString:
MSRIGKKTIV IPAGVTVTLN GSTATVKGPK GELVKEFNPE ITIKIEGNEI NVSRPTDNKN HRALHGTTRA ILNNMVVGVS EGYEKKLEL IGVGYRAQKQ GDKLVLNVGY SHPVEFVAPK GVDIEVPANT QVIVKGYNKE HVGELAANIR AVRPPEPYKG K GIRYEGEH VRRKEGKTGK

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Macromolecule #17: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 16.227671 KDa
SequenceString:
MRTTYMAKPG EVERKWYVID ATGVSLGRLS SEVASILRGK NKPQFTPHID TGDFVIIINA GKIGLTGKKA TDKIYYRHSQ YPGGLKSRT AGEMRTNNPE KLLELSIKGM LPKNSLGRQL FKKLHVYGGS EHEHAAQQPE VYELRG

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Macromolecule #18: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 13.248427 KDa
SequenceString:
MIQQESRMKV ADNSGAREVL TIKVLGGSGR KTANIGDVVV CTVKQATPGG VVKKGEVVKA VIVRTKSGAR RQDGSYIKFD ENACVIIRD DKSPRGTRIF GPVARELREN NFMKIVSLAP EVL

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Macromolecule #19: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 15.812118 KDa
SequenceString:
MKLHELKPSE GSRKERNRVG RGTGSGNGKT SGRGHKGQKA RSGGGVRLGF EGGQLPLFRR IPKRGFTNIN RKEFAIVNLD VLNRFEDGT EVTPELLVET GIIRNEKSGI KILSNGNIEK KLTVKANKFS AAAKEAIEAA GGKTEVI

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Macromolecule #20: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 16.171043 KDa
SequenceString:
MLVPKRVKYR REFRGNMRGR AKGGTEVAFG EYGLQAVEAS WITNRQIEAA RIAMTRYMKR GGKVWIKIFP HKSYTSKPIG VRMGKGKGA PEGWVSPVKR GKIMFEIAGV PEDVAREALR LAAHKLPVKT KIVKREEIGG EANES

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Macromolecule #21: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 15.246793 KDa
SequenceString:
MGYRKLGRTS SQRKALLRDL ATDLIVFERI ETTEARAKEI RKVVEKLITS GKKGDLHARR QAAAFIRHEV VEVVQVDAKG KDGSTVKKN RPVYALQKLF DDVAPRYAER QGGYTRILKK GPRRGDGAPM VIIELV

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Macromolecule #22: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 13.121936 KDa
SequenceString:
MITKIDKNKV RKKRHARVRS KISGTESRPR LNVFRSNKNI YAQIIDDVNG VTLASASNLD KDFGSAESKV DAASKVGELV AKRASEKGI TSVTFDRGGY LYHGRVKALA EAARENGLEF

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Macromolecule #23: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 13.146463 KDa
SequenceString:
MNKLIDEITK SQLNPDVPNF RPGDTVRVHA KVVEGTRERI QLFEGVVIKR RGAGISETFT VRKISNSVGV ERTFPVHTPR IAKLEVIRR GKVRRAKLYY LRNLRGKAAR IKEIR

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Macromolecule #24: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 13.71935 KDa
SequenceString:
MPRVKGGTVT RKRRKKIVKL AKGYYGSKHL LFKVANQAVM KSYQYAYRDR RQKKRDFRRL WIARINAAAR MQDLSYSKLM HGLKLAGID INRKMLADLA VNDIASFNTL ADSAKKALAK

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Macromolecule #25: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 11.234029 KDa
SequenceString:
MYAIIETGGK QIKVEAGQEI YVEKLAGEVG DVVTFDKVLF VGGDSAKVGV PFVEGATVTA KVEKQGRAKK LTVYKYKPKK NYHKKQGHR QPYTKLTIDA INA

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Macromolecule #26: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 12.895945 KDa
SequenceString:
MASEVTSAKA VAKTVRIAPR KARIVIDLIR GKQVGEAIAI LKYTPRSASP IIEKVLKSAI ANAEHNYDLD INNLVVEEAF VDEGPTLKR FRPRAQGRAS AINKRTSHIT VVVSEVKEG

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Macromolecule #27: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 10.935654 KDa
SequenceString:
MDARDIIKRP VVTEESTSIL DDKKYTFEVD TRATKTQVKY AVEEIFDVKV AKVNVMNYKG KLKRMGRYAG YTNKRRKAIV TVTADSKEI QFFEV

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Macromolecule #28: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 11.205304 KDa
SequenceString:
MHVKKGDKVK VITGKDKGKS GKVLAAFPKK DRVLIEGINM VKKHTKPSNV NPQGGILNVE APIHVSNVML LDPKTGEPTR VGYEVKGDK KVRVAKKSGE VIDK

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Macromolecule #29: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria) / Strain: ATCC BAA-679 / EGD-e
Molecular weightTheoretical: 10.57193 KDa
SequenceString:
MLKFDIQHFA HKKGGGSTSN GRDSESKRLG AKRADGQFVT GGSILYRQRG TKIYPGTNVG RGGDDTLFAK TDGVVRFERM GRDKKKVSV YPEVQEA

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Macromolecule #10: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 10 / Number of copies: 1
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 950.710438 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 UCUAUAUGGA GUU ACAAAA GAAAGUUAUA AAUGAAGCGG UCUGGAAAGG CCCGCCAAAG ACGGUAACAG CCCGGUAGUU GAAAUGGCUU UCCC UCCAG AGUGGAUCCU GAGUACGGCG 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 CUCUUUAGAG 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 UCUCGCGAAG 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 UUAGCGCGUG 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 UUAACCA

+
Macromolecule #11: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 11 / Number of copies: 1
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 36.71673 KDa
SequenceString:
CUGGUAGUUA UGGCGAGAAG GUCACACCCG UUCCCAUACC GAACACGGUA GUUAAGCUUC UCUGCGCCAA UGGUAGUUGG GGGCUUCCC CCUGCGAGAG UAGGUCGCUG CCGGG

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Macromolecule #30: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 30 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #31: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 31 / Number of copies: 1 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE / Spermidine

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Macromolecule #32: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 32 / Number of copies: 164 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #33: 1,4-DIAMINOBUTANE

MacromoleculeName: 1,4-DIAMINOBUTANE / type: ligand / ID: 33 / Number of copies: 2 / Formula: PUT
Molecular weightTheoretical: 88.151 Da
Chemical component information

ChemComp-PUT:
1,4-DIAMINOBUTANE / Putrescine

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Macromolecule #34: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 34 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
15.0 mMMg(OAc)2Magnesium acetate
95.0 mMKClPotassium chloride
5.0 mMNH4ClAmmonium chloride
0.5 mMCaCl2Calcium chloride
8.0 mMC4H12N2Putrescine
1.0 mMC7H19N3Spermidine
0.5 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid

Details: 0.05% Nikkol
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details5 OD260/mL

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.255 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 110725
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7nhn


Details: Listeria monocytogenes 70S
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 6 / Avg.num./class: 100000 / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14097
FSC plot (resolution estimation)

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