EMDB-55849: DalDroS bound to the Escherichia coli 50S ribosomal subunit

Basic information

Entry

Database: EMDB / ID: EMD-55849

• Title: DalDroS bound to the Escherichia coli 50S ribosomal subunit

Sample

• Complex: DalDroS bound to the 50S E. coli ribosomal subunit
  • Protein or peptide: x 31 types
  • RNA: x 3 types
• Ligand: x 3 types

• Keywords: DalDroS / DalDro / Dal2 / Drosocin / PrAMP / Translation / Inhibitor / Termination / NCPET / Ribosome / Cryo-EM / ANTIBIOTIC

Function / homology

Function:

translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / transcriptional attenuation / translational termination / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / cytosolic ribosome assembly / ribosome assembly / assembly of large subunit precursor of preribosome / translational initiation / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / transferase activity / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol

Domain/homology:

Peptide chain release factor 1 / : / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein L25, short-form / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / : / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L28/L24 superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / 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 L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / : / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L21-like / L21-like superfamily

Component:

Large ribosomal subunit protein uL15 / Peptide chain release factor RF1 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25

• Biological species: Escherichia coli BW25113 (bacteria) / Drosophila (fruit flies)
• Method: single particle reconstruction / cryo EM / Resolution: 2.88 Å
• Authors: Berger MJ / Safdari HA / Wilson DN

Funding support

Germany, 1 items

Organization	Grant number	Country
German Research Foundation (DFG)		Germany

• Citation: Journal: To Be Published; Title: DalDroS bound to the Escherichia coli 50S ribosomal subunit; Authors: Berger MJ / Wilson DN

History

Deposition	Nov 26, 2025	-
Header (metadata) release	May 13, 2026	-
Map release	May 13, 2026	-
Update	May 13, 2026	-
Current status	May 13, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_55849.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.83 Å

Density

Contour Level	By AUTHOR: 0.007
Minimum - Maximum	-0.021173151 - 0.054307647
Average (Standard dev.)	0.0003134066 (±0.0021495495)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 416 416 416 Spacing 416 416 416
Cell	A=B=C: 345.28 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_55849_msk_1.map

Additional map: #1

• File: emd_55849_additional_1.map

Half map: #2

• File: emd_55849_half_map_1.map

Half map: #1

• File: emd_55849_half_map_2.map

Sample components

Entire : DalDroS bound to the 50S E. coli ribosomal subunit

• Entire: Name: DalDroS bound to the 50S E. coli ribosomal subunit

Components

• Complex: DalDroS bound to the 50S E. coli ribosomal subunit
  • Protein or peptide: Large ribosomal subunit protein bL36A
  • Protein or peptide: Large ribosomal subunit protein uL3
  • Protein or peptide: Large ribosomal subunit protein bL31A
  • RNA: 23S rRNA
  • Protein or peptide: DalDroS
  • 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: Peptide chain release factor RF1
  • RNA: 5S rRNA
  • Protein or peptide: Large ribosomal subunit protein uL2
  • 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 bL9
  • Protein or peptide: Large ribosomal subunit protein uL13
  • Protein or peptide: Large ribosomal subunit protein uL14
  • Protein or peptide: 50S ribosomal protein L15
  • 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 uL24
  • Protein or peptide: 50S ribosomal protein L25
  • 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 bL32
  • Protein or peptide: Large ribosomal subunit protein uL16
  • RNA: P-site Phe-tRNA
• Ligand: ZINC ION
• Ligand: SPERMINE
• Ligand: MAGNESIUM ION

Supramolecule #1: DalDroS bound to the 50S E. coli ribosomal subunit

• Supramolecule: Name: DalDroS bound to the 50S E. coli ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#34
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)

Macromolecule #1: Large ribosomal subunit protein bL36A

• Macromolecule: Name: Large ribosomal subunit protein bL36A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 4.37739 KDa

Sequence

String:

MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG

UniProtKB: Large ribosomal subunit protein bL36A

Macromolecule #2: Large ribosomal subunit protein uL3

• Macromolecule: Name: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 22.291562 KDa

Sequence

String:

MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN (MEQ)TPGKVF KG KKMAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

UniProtKB: Large ribosomal subunit protein uL3

Macromolecule #3: Large ribosomal subunit protein bL31A

• Macromolecule: Name: Large ribosomal subunit protein bL31A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 7.887117 KDa

Sequence

String:

MKKDIHPKYE EITASCSCGN VMKIRSTVGH DLNLDVCSKC HPFFTGKQRD VATGGRVDRF NKRFNIPGSK

UniProtKB: Large ribosomal subunit protein bL31

Macromolecule #5: DalDroS

• Macromolecule: Name: DalDroS / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Drosophila (fruit flies)
• Molecular weight: Theoretical: 2.30062 KDa

Sequence

String:

GHDKPPYSPR PTSHPRPIRV

Macromolecule #6: Large ribosomal subunit protein bL33

• Macromolecule: Name: Large ribosomal subunit protein bL33 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 6.388631 KDa

Sequence

String:

MAKGIREKIK LVSSAGTGHF YTTTKNKRTK PEKLELKKFD PVVRQHVIYK EAKIK

UniProtKB: Large ribosomal subunit protein bL33

Macromolecule #7: Large ribosomal subunit protein bL34

• Macromolecule: Name: Large ribosomal subunit protein bL34 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 5.397463 KDa

Sequence

String:

MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

UniProtKB: Large ribosomal subunit protein bL34

Macromolecule #8: Large ribosomal subunit protein bL35

• Macromolecule: Name: Large ribosomal subunit protein bL35 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 7.313032 KDa

Sequence

String:

MPKIKTVRGA AKRFKKTGKG GFKHKHANLR HILTKKATKR KRHLRPKAMV SKGDLGLVIA CLPYA

UniProtKB: Large ribosomal subunit protein bL35

Macromolecule #9: Peptide chain release factor RF1

• Macromolecule: Name: Peptide chain release factor RF1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 40.573309 KDa

Sequence

String:

MKPSIVAKLE ALHERHEEVQ ALLGDAQTIA DQERFRALSR EYAQLSDVSR CFTDWQQVQE DIETAQMMLD DPEMREMAQD ELREAKEKS EQLEQQLQVL LLPKDPDDER NAFLEVRAGT GGDEAALFAG DLFRMYSRYA EARRWRVEIM SASEGEHGGY K EIIAKISG DGVYGRLKFE SGGHRVQRVP ATESQGRIHT SACTVAVMPE LPDAELPDIN PADLRIDTFR SSGAGGQHVN TT DSAIRIT HLPTGIVVEC QDERSQHKNK AKALSVLGAR IHAAEMAKRQ QAEASTRRNL LGSGDRSDRN RTYNFPQGRV TDH RINLTL YRLDEVMEGK LDMLIEPIIQ EHQADQLAAL SEQE

UniProtKB: Peptide chain release factor RF1

Macromolecule #11: Large ribosomal subunit protein uL2

• Macromolecule: Name: Large ribosomal subunit protein uL2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 29.923619 KDa

Sequence

String:

MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD GAYVTLRLRS GEMRKVEADC RATLGEVGNA EHMLRVLGKA GAARWRGVRP TVRGTAMNPV DHPHGGGEGR NF GKHPVTP WGVQTKGKKT RSNKRTDKFI VRRRSK

UniProtKB: Large ribosomal subunit protein uL2

Macromolecule #12: Large ribosomal subunit protein uL4

• Macromolecule: Name: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 22.121566 KDa

Sequence

String:

MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD VRDATGIDPV SLIAFDKVVM TADAVKQVEE MLA

UniProtKB: Large ribosomal subunit protein uL4

Macromolecule #13: Large ribosomal subunit protein uL5

• Macromolecule: Name: Large ribosomal subunit protein uL5 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 20.333611 KDa

Sequence

String:

MAKLHDYYKD EVVKKLMTEF NYNSVMQVPR VEKITLNMGV GEAIADKKLL DNAAADLAAI SGQKPLITKA RKSVAGFKIR QGYPIGCKV TLRGERMWEF FERLITIAVP RIRDFRGLSA KSFDGRGNYS MGVREQIIFP EIDYDKVDRV RGLDITITTT A KSDEEGRA LLAAFDFPFR K

UniProtKB: Large ribosomal subunit protein uL5

Macromolecule #14: Large ribosomal subunit protein uL6

• Macromolecule: Name: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 18.932791 KDa

Sequence

String:

MSRVAKAPVV VPAGVDVKIN GQVITIKGKN GELTRTLNDA VEVKHADNTL TFGPRDGYAD GWAQAGTARA LLNSMVIGVT EGFTKKLQL VGVGYRAAVK GNVINLSLGF SHPVDHQLPA GITAECPTQT EIVLKGADKQ VIGQVAADLR AYRRPEPYKG K GVRYADEV VRTKEAKKK

UniProtKB: Large ribosomal subunit protein uL6

Macromolecule #15: Large ribosomal subunit protein bL9

• Macromolecule: Name: Large ribosomal subunit protein bL9 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 15.78902 KDa

Sequence

String:

MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE

UniProtKB: Large ribosomal subunit protein bL9

Macromolecule #16: Large ribosomal subunit protein uL13

• Macromolecule: Name: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 16.050606 KDa

Sequence

String:

MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI

UniProtKB: Large ribosomal subunit protein uL13

Macromolecule #17: Large ribosomal subunit protein uL14

• Macromolecule: Name: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 13.565067 KDa

Sequence

String:

MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEVL

UniProtKB: Large ribosomal subunit protein uL14

Macromolecule #18: 50S ribosomal protein L15

• Macromolecule: Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 15.008471 KDa

Sequence

String:

MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF EGGQMPLYRR LPKFGFTSRK AAITAEIRLS DLAKVEGGV VDLNTLKAAN IIGIQIEFAK VILAGEVTTP VTVRGLRVTK GARAAIEAAG GKIEE

UniProtKB: Large ribosomal subunit protein uL15

Macromolecule #19: Large ribosomal subunit protein bL17

• Macromolecule: Name: Large ribosomal subunit protein bL17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 14.393657 KDa

Sequence

String:

MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS EKAEAAAE

UniProtKB: Large ribosomal subunit protein bL17

Macromolecule #20: Large ribosomal subunit protein uL18

• Macromolecule: Name: Large ribosomal subunit protein uL18 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 12.794668 KDa

Sequence

String:

MDKKSARIRR ATRARRKLQE LGATRLVVHR TPRHIYAQVI APNGSEVLVA ASTVEKAIAE QLKYTGNKDA AAAVGKAVAE RALEKGIKD VSFDRSGFQY HGRVQALADA AREAGLQF

UniProtKB: Large ribosomal subunit protein uL18

Macromolecule #21: Large ribosomal subunit protein bL19

• Macromolecule: Name: Large ribosomal subunit protein bL19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 13.159278 KDa

Sequence

String:

MSNIIKQLEQ EQMKQDVPSF RPGDTVEVKV WVVEGSKKRL QAFEGVVIAI RNRGLHSAFT VRKISNGEGV ERVFQTHSPV VDSISVKRR GAVRKAKLYY LRERTGKAAR IKERLN

UniProtKB: Large ribosomal subunit protein bL19

Macromolecule #22: Large ribosomal subunit protein bL20

• Macromolecule: Name: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 13.528024 KDa

Sequence

String:

MARVKRGVIA RARHKKILKQ AKGYYGARSR VYRVAFQAVI KAGQYAYRDR RQRKRQFRQL WIARINAAAR QNGISYSKFI NGLKKASVE IDRKILADIA VFDKVAFTAL VEKAKAALA

UniProtKB: Large ribosomal subunit protein bL20

Macromolecule #23: Large ribosomal subunit protein bL21

• Macromolecule: Name: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 11.586374 KDa

Sequence

String:

MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

UniProtKB: Large ribosomal subunit protein bL21

Macromolecule #24: Large ribosomal subunit protein uL22

• Macromolecule: Name: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 12.253359 KDa

Sequence

String:

METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

UniProtKB: Large ribosomal subunit protein uL22

Macromolecule #25: Large ribosomal subunit protein uL23

• Macromolecule: Name: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 11.22216 KDa

Sequence

String:

MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNLDFVGGA E

UniProtKB: Large ribosomal subunit protein uL23

Macromolecule #26: Large ribosomal subunit protein uL24

• Macromolecule: Name: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 11.33925 KDa

Sequence

String:

MAAKIRRDDE VIVLTGKDKG KRGKVKNVLS SGKVIVEGIN LVKKHQKPVP ALNQPGGIVE KEAAIQVSNV AIFNAATGKA DRVGFRFED GKKVRFFKSN SETIK

UniProtKB: Large ribosomal subunit protein uL24

Macromolecule #27: 50S ribosomal protein L25

• Macromolecule: Name: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 10.713465 KDa

Sequence

String:

MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA

UniProtKB: Large ribosomal subunit protein bL25

Macromolecule #28: Large ribosomal subunit protein bL27

• Macromolecule: Name: Large ribosomal subunit protein bL27 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 9.14654 KDa

Sequence

String:

MAHKKAGGST RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE

UniProtKB: Large ribosomal subunit protein bL27

Macromolecule #29: Large ribosomal subunit protein bL28

• Macromolecule: Name: Large ribosomal subunit protein bL28 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 9.027551 KDa

Sequence

String:

MSRVCQVTGK RPVTGNNRSH ALNATKRRFL PNLHSHRFWV ESEKRFVTLR VSAKGMRVID KKGIDTVLAE LRARGEKY

UniProtKB: Large ribosomal subunit protein bL28

Macromolecule #30: Large ribosomal subunit protein uL29

• Macromolecule: Name: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 7.286464 KDa

Sequence

String:

MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

UniProtKB: Large ribosomal subunit protein uL29

Macromolecule #31: Large ribosomal subunit protein uL30

• Macromolecule: Name: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 6.55482 KDa

Sequence

String:

MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE

UniProtKB: Large ribosomal subunit protein uL30

Macromolecule #32: Large ribosomal subunit protein bL32

• Macromolecule: Name: Large ribosomal subunit protein bL32 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 6.463445 KDa

Sequence

String:

MAVQQNKPTR SKRGMRRSHD ALTAVTSLSV DKTSGEKHLR HHITADGYYR GRKVIAK

UniProtKB: Large ribosomal subunit protein bL32

Macromolecule #33: Large ribosomal subunit protein uL16

• Macromolecule: Name: Large ribosomal subunit protein uL16 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 15.343327 KDa

Sequence

String:

MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV (4D4)(MS6)GKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM

UniProtKB: Large ribosomal subunit protein uL16

Macromolecule #4: 23S rRNA

• Macromolecule: Name: 23S rRNA / type: rna / ID: 4 / Number of copies: 1
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 941.811562 KDa

Sequence

String:

GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAU(1MG)(PSU)(5MU)GAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCA AU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACU G UUUCGGCAAG GGGGUCAUCC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACAC GGCGGG(PSU)GCU AACGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUG GGA AACGAUGUGG GAAGGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCAC UG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUU G GGUAGGGGAG CGUUCUGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUA AGUAACGAUA AAGCGGGUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUA AGGCGAGGCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG G GGACGGAG AAGGCUAUGU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AA AUCAAGG CUGAGGCGUG AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAU CAGGUA ACAUCAAAUC GUACCCCAAA CCGACAC(6MZ)GG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAA CUAGGCAAAA UGGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCCU CGCGGAUGGA G CUGAAAUC AGUCGAAGAU ACCAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AU ACGGUGU GACGCCU(2MG)CC CGGUGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCG GUAAACGGCG GCCG(PSU)AAC(3TD)A (PSU)AACGGUCCU AAGGUAGCGA AA(5MU)UCCUUGU CGGGUAAGUU CCGA C(5MC)UGC ACGAAUGGCG UAAUGAUGGC CAGGCUGUCU CCACCCGAGA CUCAGUGAAA UUGAACUCGC UGUG(6MZ)AG AU GCAGUGUACC CGCGGCAAGA CGGAAAGACC CCGU(G7M)AACCU UUACUAUAGC UUGACACUGA ACAUUGAGCC UUGA UGUGU AGGAUAGGUG GGAGGCUUUG AAGUGUGGAC GCCAGUCUGC AUGGAGCCGA CCUUGAAAUA CCACCCUUUA AUGUU UGAU GUUCUAACGU UGACCCGUAA UCCGGGUUGC GGACAGUGUC UGGUGGGUAG UUUGACUG(OMG)G GCGGUCUCCU CC UAAAGAG UAACGGAGGA GCACGAAGGU UGGCUAAUCC UGGUCGGACA UCAGGAGGUU AGUGCAAUGG CAUAAGCCAG CUU GACUGC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUC AACGG AUAAAAGGUA CUCCG(2MG)GGA(H2U) AACAGGC(PSU)GA UACCGCCCAA GAGUUCAUAU CGACGGCGGU GUU UGGCA(OMC) CUCG(2MA)(PSU)GUCG GCUCAUCACA UCCUGGGGCU GAAGUAGGUC CCAAGGGUAU GGC(OMU)GUUC G CCAUUUAAAG UGGUACGCGA GC(PSU)GGGUUUA GAACGUCGUG AGACAG(PSU)(PSU)CG GUCCCUAUCU GCCGUGG GC GCUGGAGAAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCC A AUGGCACUGC CCGGUAGCUA AAUGCGGAAG AGAUAAGUGC UGAAAGCAUC UAAGCACGAA ACUUGCCCCG AGAUGAGUU CUCCCUGACC CUUUAAGGGU CCUGAAGGAA CGUUGAAGAC GACGACGUUG AUAGGCCGGG UGUGUAAGCG CAGCGAUGCG UUGAGCUAA CCGGUACUAA UGAACCGUGA GGCUUAACCU U

Macromolecule #10: 5S rRNA

• Macromolecule: Name: 5S rRNA / type: rna / ID: 10 / Number of copies: 1
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 38.79009 KDa

Sequence

String:

UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCU CCCCAUGCGA GAGUAGGGAA CUGCCAGGCA U

GENBANK: GENBANK: CP053605.1

Macromolecule #34: P-site Phe-tRNA

• Macromolecule: Name: P-site Phe-tRNA / type: rna / ID: 34 / Number of copies: 1
• Source (natural): Organism: Escherichia coli BW25113 (bacteria)
• Molecular weight: Theoretical: 24.485539 KDa

Sequence

String:

GCCCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUGAAAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGG GCACCA

Macromolecule #35: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 35 / Number of copies: 2 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #36: SPERMINE

• Macromolecule: Name: SPERMINE / type: ligand / ID: 36 / Number of copies: 1 / Formula: SPM
• Molecular weight: Theoretical: 202.34 Da

Chemical component information

ChemComp-SPM:
SPERMINE

Macromolecule #37: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 37 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.4
• Vitrification: Cryogen name: ETHANE-PROPANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.14 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.3 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

7k00

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number images used: 202610
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD