EMDB-14864: 70S E. coli ribosome with truncated uL23 and uL24 loops

Basic information

Entry

Database: EMDB / ID: EMD-14864

• Title: 70S E. coli ribosome with truncated uL23 and uL24 loops
• Map data: Main map

Sample

• Complex: E coli ribosome with uL23 and uL24 loop truncation
  • Protein or peptide: x 28 types
  • RNA: x 2 types

• Keywords: ribosome / exit tunnel / structural modification / ribosomal protein

Function / homology

Function:

transcriptional attenuation / endoribonuclease inhibitor activity / 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 / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm

Domain/homology:

Ribosomal protein L25, short-form / : / 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 L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 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 L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / 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 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 L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal

Component:

Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / 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 uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL27

• Biological species: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) / Escherichia coli (E. coli)
• Method: single particle reconstruction / cryo EM / Resolution: 2.7 Å
• Authors: Mitropoulou A / Wlodarski T / Ahn M / Becker TA / Beckmann R / Cabrita LD / Christodoulou J

Funding support

United Kingdom, 1 items

Organization	Grant number	Country
Wellcome Trust	206409/Z/17/Z	United Kingdom

• Citation: Journal: Nat Commun / Year: 2022; Title: Modulating co-translational protein folding by rational design and ribosome engineering.; Authors: Minkoo Ahn / Tomasz Włodarski / Alkistis Mitropoulou / Sammy H S Chan / Haneesh Sidhu / Elena Plessa / Thomas A Becker / Nediljko Budisa / Christopher A Waudby / Roland Beckmann / Anaïs M E Cassaignau / Lisa D Cabrita / John Christodoulou / ; Abstract: Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by the shape and surface of the narrow tunnel, we have rationally engineered three exit tunnel protein loops (uL22, uL23 and uL24) of the 70S ribosome by CRISPR/Cas9 gene editing, and studied the co-translational folding of an immunoglobulin-like filamin domain (FLN5). Our thermodynamics measurements employing F/N/methyl-TROSY NMR spectroscopy together with cryo-EM and molecular dynamics simulations reveal how the variations in the lengths of the loops present across species exert their distinct effects on the free energy of FLN5 folding. A concerted interplay of the uL23 and uL24 loops is sufficient to alter co-translational folding energetics, which we highlight by the opposite folding outcomes resulting from their extensions. These subtle modulations occur through a combination of the steric effects relating to the shape of the tunnel, the dynamic interactions between the ribosome surface and the unfolded nascent chain, and its altered exit pathway within the vestibule. These results illustrate the role of the exit tunnel structure in co-translational folding, and provide principles for how to remodel it to elicit a desired folding outcome.

History

Deposition	Apr 29, 2022	-
Header (metadata) release	Aug 10, 2022	-
Map release	Aug 10, 2022	-
Update	Nov 13, 2024	-
Current status	Nov 13, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_14864.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Main map
• Voxel size: X=Y=Z: 1.085 Å

Density

Contour Level	By AUTHOR: 0.0885
Minimum - Maximum	-0.13628478 - 0.53549933
Average (Standard dev.)	-0.00897642 (±0.027543541)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 368 368 368 Spacing 368 368 368
Cell	A=B=C: 399.28003 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_14864_msk_1.map

Additional map: Unsharpened map

• File: emd_14864_additional_1.map
• Annotation: Unsharpened map

Half map: Half map 1

• File: emd_14864_half_map_1.map
• Annotation: Half map 1

Half map: #1

• File: emd_14864_half_map_2.map

Sample components

Entire : E coli ribosome with uL23 and uL24 loop truncation

• Entire: Name: E coli ribosome with uL23 and uL24 loop truncation

Components

• Complex: E coli ribosome with uL23 and uL24 loop truncation
  • 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 L32
  • Protein or peptide: 50S ribosomal protein L33
  • Protein or peptide: 50S ribosomal protein L34
  • Protein or peptide: 50S ribosomal protein L35
  • Protein or peptide: 50S ribosomal protein L36
  • RNA: 5S rRNA
  • RNA: 23S rRNA
  • 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 L9
  • 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 L25
  • Protein or peptide: 50S ribosomal protein L27

Supramolecule #1: E coli ribosome with uL23 and uL24 loop truncation

• Supramolecule: Name: E coli ribosome with uL23 and uL24 loop truncation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
• Source (natural): Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

Macromolecule #1: 50S ribosomal protein L28

• Macromolecule: Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 9.027551 KDa

Sequence

String:

MSRVCQVTGK RPVTGNNRSH ALNATKRRFL PNLHSHRFWV ESEKRFVTLR VSAKGMRVID KKGIDTVLAE LRARGEKY

UniProtKB: Large ribosomal subunit protein bL28

Macromolecule #2: 50S ribosomal protein L29

• Macromolecule: Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 7.286464 KDa

Sequence

String:

MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

UniProtKB: Large ribosomal subunit protein uL29

Macromolecule #3: 50S ribosomal protein L30

• Macromolecule: Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 6.55482 KDa

Sequence

String:

MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE

UniProtKB: Large ribosomal subunit protein uL30

Macromolecule #4: 50S ribosomal protein L32

• Macromolecule: Name: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 6.463445 KDa

Sequence

String:

MAVQQNKPTR SKRGMRRSHD ALTAVTSLSV DKTSGEKHLR HHITADGYYR GRKVIAK

UniProtKB: Large ribosomal subunit protein bL32

Macromolecule #5: 50S ribosomal protein L33

• Macromolecule: Name: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 6.388631 KDa

Sequence

String:

MAKGIREKIK LVSSAGTGHF YTTTKNKRTK PEKLELKKFD PVVRQHVIYK EAKIK

UniProtKB: Large ribosomal subunit protein bL33

Macromolecule #6: 50S ribosomal protein L34

• Macromolecule: Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 5.397463 KDa

Sequence

String:

MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

UniProtKB: Large ribosomal subunit protein bL34

Macromolecule #7: 50S ribosomal protein L35

• Macromolecule: Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 7.313032 KDa

Sequence

String:

MPKIKTVRGA AKRFKKTGKG GFKHKHANLR HILTKKATKR KRHLRPKAMV SKGDLGLVIA CLPYA

UniProtKB: Large ribosomal subunit protein bL35

Macromolecule #8: 50S ribosomal protein L36

• Macromolecule: Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 4.37739 KDa

Sequence

String:

MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG

Macromolecule #11: 50S ribosomal protein L2

• Macromolecule: Name: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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: 50S ribosomal protein L3

• Macromolecule: Name: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 22.277535 KDa

Sequence

String:

MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

UniProtKB: Large ribosomal subunit protein uL3

Macromolecule #13: 50S ribosomal protein L4

• Macromolecule: Name: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #14: 50S ribosomal protein L5

• Macromolecule: Name: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #15: 50S ribosomal protein L6

• Macromolecule: Name: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #16: 50S ribosomal protein L9

• Macromolecule: Name: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #17: 50S ribosomal protein L13

• Macromolecule: Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #18: 50S ribosomal protein L14

• Macromolecule: Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #19: 50S ribosomal protein L15

• Macromolecule: Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #20: 50S ribosomal protein L16

• Macromolecule: Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 15.312269 KDa

Sequence

String:

MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV RMGKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM

UniProtKB: Large ribosomal subunit protein uL16

Macromolecule #21: 50S ribosomal protein L17

• Macromolecule: Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #22: 50S ribosomal protein L18

• Macromolecule: Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #23: 50S ribosomal protein L19

• Macromolecule: Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #24: 50S ribosomal protein L20

• Macromolecule: Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #25: 50S ribosomal protein L21

• Macromolecule: Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #26: 50S ribosomal protein L22

• Macromolecule: Name: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #27: 50S ribosomal protein L23

• Macromolecule: Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 10.414235 KDa

Sequence

String:

MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRR SDWKKAYVTL KEGQNLDFV GGAE

UniProtKB: Large ribosomal subunit protein uL23

Macromolecule #28: 50S ribosomal protein L24

• Macromolecule: Name: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 10.207946 KDa

Sequence

String:

MAAKIRRDDE VIVLTGKDKG KRGKVKNVLS SGKVIVEGIN LVKKHGIVEK EAAIQVSNVA IFNAATGKAD RVGFRFEDGK KVRFFKSNS ETIK

Macromolecule #29: 50S ribosomal protein L25

• Macromolecule: Name: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• 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 #30: 50S ribosomal protein L27

• Macromolecule: Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 9.14654 KDa

Sequence

String:

MAHKKAGGST RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE

UniProtKB: Large ribosomal subunit protein bL27

Macromolecule #9: 5S rRNA

• Macromolecule: Name: 5S rRNA / type: rna / ID: 9 / Number of copies: 1
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 38.79009 KDa

Sequence

String:

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

GENBANK: GENBANK: CP035706.1

Macromolecule #10: 23S rRNA

• Macromolecule: Name: 23S rRNA / type: rna / ID: 10 / Number of copies: 1
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 941.620438 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 AAUGUUGAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCAAUC AAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAUCC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACACG GCGGGUGCUA A CGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUGGGAA ACGAUGUGGG AA GGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCACUGG UCGAGUCGGC CUG CGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUC UGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUAA GUAACGAUAA AGCGG GUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUAA GGCGAG GCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG GGGACGGAGA AGGCUAU GU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AAAUCAAGGC UGAGGCGU G AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAUCAGGUAA CAUCAAAUC GUACCCCAAA CCGACACAGG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAAGCGACU UGCUCGUGGA GCUGAAAUCA GUCGAAGAUA C CAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AUACGGUGUG ACGCCUGCCC GG UGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCGG UAAACGGCGG CCGUAACUAU AAC GGUCCU AAGGUAGCGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACC CGAGA CUCAGUGAAA UUGAACUCGC UGUGAAGAUG CAGUGUACCC GCGGCAAGAC GGAAAGACCC CGUGAACCUU UACUA UAGC UUGACACUGA ACAUUGAGCC UUGAUGUGUA GGAUAGGUGG GAGGCUUAGA AGUGUGGACG CCAGUCUGCA UGGAGC CGA CCUUGAAAUA CCACCCUUUA AUGUUUGAUG UUCUAACGUU GACCCGUAAU CCGGGUUGCG GACAGUGUCU GGUGGGU AG UUUGACUGGG GCGGUCUCCU CCUAAAGAGU AACGGAGGAG CACGAAGGUU GGCUAAUCCU GGUCGGACAU CAGGAGGU U AGUGCAAUGG CAUAAGCCAG CUUGACUGCG AGCGUGACGG CGCGAGCAGG UGCGAAAGCA GGUCAUAGUG AUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCGGGGAUA ACAGGCUGAU ACCGCCCAAG AGUUCAUAUC GACGGCGGU GUUUGGCACC UCGAUGUCGG CUCAUCACAU CCUGGGGCUG AAGUAGGUCC CAAGGGUGAU GCUGUUCGCC A UUUAAAGU GGUACGCGAG CUGGGUUUAG AACGUCGUGA GACAGUUCGG UCCCUAUCUG CCGUGGGCGC UGGAGAACUG AG GGGGGCU GCUCCUAGUA CGAGAGGACC GGAGUGGACG CAUCACUGGU GUUCGGGUUG UCAUGCCAAU GGCACUGCCC GGU AGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAA GGGUC CUGAAGGAAC GUUGAAGACG ACGACGUUGA UAGGCCGGGU GUGUAAGCGC AGCGAUGCGU UGAGCUAACC GGUAC UAAU GAACCGUGAG GCUUAACCUU

GENBANK: GENBANK: CP077969.1

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 95 %

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.9 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: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: INSILICO MODEL
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131042
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION