EMDB-11862: Structure of the bacterial RQC complex (Decoding State)

Basic information

• Entry: Database: EMDB / ID: EMD-11862
• Title: Structure of the bacterial RQC complex (Decoding State)

Sample

• Complex: Bacterial RQC complex
  • RNA: x 3 types
  • Protein or peptide: x 30 types

• Keywords: RIBOSOME / rqch / rqc / rqc2 / hsp15 / fibronectin-binding protein / NEMF / ribosome-associated quality control / ribosome-associated / 50s / Alanine-tailing

Function / homology

Function:

RQC complex / positive regulation of rRNA processing / nucleoid / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / transferase activity / 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 / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / DNA binding / RNA binding / cytoplasm

Domain/homology:

RNA-binding protein, HP1423 type / Rqc2 homolog RqcH, bacterial / : / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 signature. / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / : / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / 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.

Component:

Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Rqc2 homolog RqcH / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL21 / RQC P-site tRNA stabilizing factor / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL11

• Biological species: Bacillus subtilis subsp. subtilis str. 168 (bacteria) / Bacillus subtilis (strain 168) (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 2.99 Å
• Authors: Filbeck S / Pfeffer S

Funding support

Germany, United States, 2 items

Organization	Grant number	Country
German Research Foundation (DFG)	SFB1036	Germany
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	R01 NS102414	United States

• Citation: Journal: Mol Cell / Year: 2021; Title: Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC.; Authors: Sebastian Filbeck / Federico Cerullo / Helge Paternoga / George Tsaprailis / Claudio A P Joazeiro / Stefan Pfeffer / ; Abstract: Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved RQC factor, senses the obstruction and recruits tRNA to modify nascent-chain C termini with a polyalanine degron. However, how RqcH and its eukaryotic homologs (Rqc2 and NEMF), despite their relatively simple architecture, synthesize such C-terminal tails in the absence of a small ribosomal subunit and mRNA has remained unknown. Here, we present cryoelectron microscopy (cryo-EM) structures of Bacillus subtilis RQC complexes representing different Ala tail synthesis steps. The structures explain how tRNA is selected via anticodon reading during recruitment to the A-site and uncover striking hinge-like movements in RqcH leading tRNA into a hybrid A/P-state associated with peptidyl-transfer. Finally, we provide structural, biochemical, and molecular genetic evidence identifying the Hsp15 homolog (encoded by rqcP) as a novel RQC component that completes the cycle by stabilizing the P-site tRNA conformation. Ala tailing thus follows mechanistic principles surprisingly similar to canonical translation elongation.

History

Deposition	Oct 21, 2020	-
Header (metadata) release	Nov 25, 2020	-
Map release	Nov 25, 2020	-
Update	May 1, 2024	-
Current status	May 1, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_11862.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.07 Å

Density

Contour Level	By AUTHOR: 0.011 / Movie #1: 0.02
Minimum - Maximum	-0.041586697 - 0.30001622
Average (Standard dev.)	0.00048054146 (±0.004808396)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 384 384 384 Spacing 384 384 384
Cell	A=B=C: 410.88 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.07	1.07	1.07
M x/y/z	384	384	384
origin x/y/z	0.000	0.000	0.000
length x/y/z	410.880	410.880	410.880
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	240	240	240
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	384	384	384
D min/max/mean	-0.042	0.300	0.000

Supplemental data

Sample components

Entire : Bacterial RQC complex

• Entire: Name: Bacterial RQC complex

Components

• Complex: Bacterial RQC complex
  • 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 L11
  • 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
  • RNA: Ala-tRNA (P-site)
  • Protein or peptide: 50S ribosomal protein L20
  • Protein or peptide: Rqc2 homolog RqcH
  • Protein or peptide: 50S ribosomal protein L22
  • Protein or peptide: 50S ribosomal protein L24
  • Protein or peptide: 50S ribosomal protein L27
  • Protein or peptide: nascent polyalanine
  • Protein or peptide: 50S ribosomal protein L28
  • Protein or peptide: Uncharacterized protein YabO
  • Protein or peptide: 50S ribosomal protein L30
  • Protein or peptide: 50S ribosomal protein L19
  • Protein or peptide: 50S ribosomal protein L32
  • Protein or peptide: 50S ribosomal protein L33 1
  • Protein or peptide: 50S ribosomal protein L34
  • Protein or peptide: 50S ribosomal protein L35
  • Protein or peptide: 50S ribosomal protein L36
  • Protein or peptide: 50S ribosomal protein L21
  • Protein or peptide: 50S ribosomal protein L23
  • Protein or peptide: 50S ribosomal protein L29

Supramolecule #1: Bacterial RQC complex

• Supramolecule: Name: Bacterial RQC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#33
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Macromolecule #1: 23S ribosomal RNA

• Macromolecule: Name: 23S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 914.625938 KDa

Sequence

String:

UUAAGUUAGA AAGGGCGCAC GGUGGAUGCC UUGGCACUAG GAGCCGAUGA AGGACGGGAC GAACACCGAU AUGCUUCGGG GAGCUGUAA GCAAGCUUUG AUCCGGAGAU UUCCGAAUGG GGAAACCCAC CACUCGUAAU GGAGUGGUAU CCAUAUCUGA A UUCAUAGG AUAUGAGAAG GCAGACCCGG GGAACUGAAA CAUCUAAGUA CCCGGAGGAA GAGAAAGCAA AUGCGAUUCC CU GAGUAGC GGCGAGCGAA ACGGGAUCAG CCCAAACCAA GAGGCUUGCC UCUUGGGGUU GUAGGACACU CUGUACGGAG UUA CAAAGG AACGAGGUAG AUGAAGAGGU CUGGAAAGGC CCGCCAUAGG AGGUAACAGC CCUGUAGUCA AAACUUCGUU CUCU CCUGA GUGGAUCCUG AGUACGGCGG AACACGUGAA AUUCCGUCGG AAUCCGGGAG GACCAUCUCC CAAGGCUAAA UACUC CCUA GUGACCGAUA GUGAACCAGU ACCGUGAGGG AAAGGUGAAA AGCACCCCGG AAGGGGAGUG AAAGAGAUCC UGAAAC CGU GUGCCUACAA GUAGUCAGAG CCCGUUAACG GGUGAUGGCG UGCCUUUUGU AGAAUGAACC GGCGAGUUAC GAUCUCG UG CAAGGUUAAG CAGAAGAUGC GGAGCCGCAG CGAAAGCGAG UCUGAAUAGG GCGCAUGAGU ACGUGGUCGU AGACCCGA A ACCAGGUGAU CUACCCAUGU CCAGGGUGAA GUUCAGGUAA CACUGAAUGG AGGCCCGAAC CCACGCACGU UGAAAAGUG CGGGGAUGAG GUGUGGGUAG GGGUGAAAUG CCAAUCGAAC CUGGAGAUAG CUGGUUCUCU CCGAAAUAGC UUUAGGGCUA GCCUCAAGG UAAGAGUCUU GGAGGUAGAG CACUGAUUGG ACUAGGGGCC CCUACCGGGU UACCGAAUUC AGUCAAACUC C GAAUGCCA AUGACUUAUC CUUGGGAGUC AGACUGCGAG UGAUAAGAUC CGUAGUCGAA AGGGAAACAG CCCAGACCGC CA GCUAAGG UCCCAAAGUA UACGUUAAGU GGAAAAGGAU GUGGAGUUGC UUAGACAACC AGGAUGUUGG CUUAGAAGCA GCC ACCAUU UAAAGAGUGC GUAAUAGCUC ACUGGUCGAG UGACUCUGCG CCGAAAAUGU ACCGGGGCUA AACGUAUCAC CGAA GCUGC GGACUGUUCU UCGAACAGUG GUAGGAGAGC GUUCUAAGGG CUGUGAAGCC AGACCGGAAG GACUGGUGGA GCGCU UAGA AGUGAGAAUG CCGGUAUGAG UAGCGAAAGA GGGGUGAGAA UCCCCUCCAC CGAAUGCCUA AGGUUUCCUG AGGAAG GCU CGUCCGCUCA GGGUUAGUCG GGACCUAAGC CGAGGCCGAA AGGCGUAGGC GAUGGACAAC AGGUUGAUAU UCCUGUA CC ACCUCCUCAC CAUUUGAGCA AUGGGGGGAC GCAGGAGGAU AGGGUAAGCG CGGUAUUGGA UAUCCGCGUC CAAGCAGU U AGGCUGGGAA AUAGGCAAAU CCGUUUCCCA UAAGCCUGAG CUGUGAUGGC GAGCGAAAUA UAGUAGCGAA GUUCCUGAU UCCACACUGC CAAGAAAAGC CUCUAGCGAG GUGAGAGGUG CCCGUACCGC AAACCGACAC AGGUAGGCGA GGAGAGAAUC CUAAGGUGA UCGAGAGAAC UCUCGUUAAG GAACUCGGCA AAAUGACCCC GUAACUUCGG GAGAAGGGGU GCUCUGUUAG G GUGCAAGC CCGAGAGAGC CGCAGUGAAU AGGCCCAGGC GACUGUUUAG CAAAAACACA GGUCUCUGCG AAGCCGUAAG GC GAAGUAU AGGGGCUGAC GCCUGCCCGG UGCUGGAAGG UUAAGAGGAG CGCUUAGCGU AAGCGAAGGU GCGAAUUGAA GCC CCAGUA AACGGCGGCC GUAAACGGUC CUAAGGUAGC GAAAUUCCUU GUCGGGUAAG UUCCGACCCG CACGAAAGGC GCAA CGAUC UGGGCACUGU CUCAACGAGA GACUCGGUGA AAUUAUAGUA CCUGUGAAGA UGCAGGUUAC CCGCGACAGG ACGGA AAGA CCCCGUGGAG CUUUACUGCA GCCUGAUAUU GAAUUCUAAC CCGCCGCCCU UAUCGGGCGG GGAGACAGUG UCAGGU GGG CAGUUUGACU GGGGCGGUCG CCUCCUAAAA GGUAACGGAG GCGCCCAAAG GUUCCCUCAG AAUGGUUGGA AAUCAUU CG CAGAGUGUAA AGGCACAAGG GAGCUUGACU GCGAGACCUA CAAGUCGAGC AGGGACGAAA GUCGGGCUUA GUGAUCCG G UGGUUCCGCA UGGAAGGGCC AUCGCUCAAC GGAUAAAAGC UACCCCGGGG AUAACAGGCU UAUCUCCCCC AAGAGUCCA CAUCGACGGG GAGGUUUGGC ACCUCGAUGU CGGCUCAUCG CAUCCUGGGG CUGUAGUCGG UCCCAAGGGU UGGGCUGUUC GCCCAUUAA AGCGGUACGC GAGCUGGGUU CAGAACGUCG UGAGACAGUU CGGUCCCUAU CCGUCGCGGG CGCAGGAAAU U UGAGAGGA GCUGUCCUUA GUACGAGAGG ACCGGGAUGG ACGCACCGCU GGUGUACCAG UUGUUCUGCC AAGGGCAUCG CU GGGUAGC UAUGUGCGGA CGGGAUAAGU GCUGAAAGCA UCUAAGCAUG AAGCCCCCCU CAAGAUGAGA UUUCCCAUUC CGC AAGGAA GUAAGAUCCC UGAAAGAUGA UCAGGUUGAU AGGUCUGAGG UGGAAGUGUG GCGACACAUG GAGCUGACAG AUAC UAAUC GAUCGAGGAC UUAAC

Macromolecule #2: 5S ribosomal RNA

• Macromolecule: Name: 5S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 36.15752 KDa

Sequence

String:

UGGUGGCGAU AGCGAAGAGG UCACACCCGU UCCCAUACCG AACACGGAAG UUAAGCUCUU CAGCGCCGAU GGUAGUCGGG GGUUUCCCC CUGUGAGAGU AGGACGCCGC CAA

GENBANK: GENBANK: CP019662.1

Macromolecule #15: Ala-tRNA (P-site)

• Macromolecule: Name: Ala-tRNA (P-site) / type: rna / ID: 15 / Number of copies: 2
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 24.491547 KDa

Sequence

String:

GGGGCCUUAG CUCAGCUGGG AGAGCGCCUG CUUUGCACGC AGGAGGUCAG CGGUUCGAUC CCGCUAGGCU CCACCA

Macromolecule #3: 50S ribosomal protein L2

• Macromolecule: Name: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 30.335125 KDa

Sequence

String:

MAIKKYKPTS NGRRGMTTSD FAEITTDKPE KSLLAPLHKK GGRNNQGKLT VRHQGGGHKR QYRVIDFKRD KDGIPGRVAT VEYDPNRSA NIALINYADG EKRYILAPKG IQVGTEIMSG PEADIKVGNA LPLINIPVGT VVHNIELKPG KGGQLVRSAG T SAQVLGKE GKYVLVRLNS GEVRMILSAC RASIGQVGNE QHELINIGKA GRSRWKGIRP TVRGSVMNPN DHPHGGGEGR AP IGRKSPM SPWGKPTLGF KTRKKKNKSD KFIVRRRKNK

UniProtKB: Large ribosomal subunit protein uL2

Macromolecule #4: 50S ribosomal protein L3

• Macromolecule: Name: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 22.723348 KDa

Sequence

String:

MTKGILGRKI GMTQVFAENG DLIPVTVIEA APNVVLQKKT AENDGYEAIQ LGFDDKREKL SNKPEKGHVA KAETAPKRFV KELRGVEMD AYEVGQEVKV EIFSAGEIVD VTGVSKGKGF QGAIKRHGQS RGPMSHGSRY HRRPGSMGPV DPNRVFKGKL L PGRMGGEQ ITVQNLEIVK VDAERNLLLI KGNVPGAKKS LITVKSAVKS K

UniProtKB: Large ribosomal subunit protein uL3

Macromolecule #5: 50S ribosomal protein L4

• Macromolecule: Name: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 22.424951 KDa

Sequence

String:

MPKVALYNQN GSTAGDIELN ASVFGIEPNE SVVFDAILMQ RASLRQGTHK VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVV FGPTPRSYSY KLPKKVRRLA IKSVLSSKVI DNNIIVLEDL TLDTAKTKEM AAILKGLSVE KKALIVTADA N EAVALSAR NIPGVTVVEA NGINVLDVVN HEKLLITKAA VEKVEEVLA

UniProtKB: Large ribosomal subunit protein uL4

Macromolecule #6: 50S ribosomal protein L5

• Macromolecule: Name: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 20.177564 KDa

Sequence

String:

MNRLKEKYNK EIAPALMTKF NYDSVMQVPK IEKIVINMGV GDAVQNAKAI DSAVEELTFI AGQKPVVTRA KKSIAGFRLR EGMPIGAKV TLRGERMYDF LDKLISVSLP RVRDFRGVSK KSFDGRGNYT LGIKEQLIFP EIDYDKVTKV RGMDIVIVTT A NTDEEARE LLTQVGMPFQ K

UniProtKB: Large ribosomal subunit protein uL5

Macromolecule #7: 50S ribosomal protein L6

• Macromolecule: Name: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 19.543389 KDa

Sequence

String:

MSRVGKKLLE IPSDVTVTLN DNNTVAVKGP KGELTRTFHP DMEIKVEDNV LTVARPSDQK EHRALHGTTR SLLGNMVEGV SKGFERGLE LVGVGYRASK SGNKLVLNVG YSHPVEIVPE EGIEIEVPSQ TKVVVKGTDK ERVGAIAANI RAVRSPEPYK G KGIRYEGE VVRRKEGKSA K

UniProtKB: Large ribosomal subunit protein uL6

Macromolecule #8: 50S ribosomal protein L11

• Macromolecule: Name: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 14.951442 KDa

Sequence

String:

MAKKVVKVVK LQIPAGKANP APPVGPALGQ AGVNIMGFCK EFNARTADQA GLIIPVEISV YEDRSFTFIT KTPPAAVLLK KAAGIESGS GEPNRNKVAT VKRDKVREIA ETKMPDLNAA DVEAAMRMVE GTARSMGIVI ED

UniProtKB: Large ribosomal subunit protein uL11

Macromolecule #9: 50S ribosomal protein L13

• Macromolecule: Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 16.407104 KDa

Sequence

String:

MRTTPMANAS TIERKWLVVD AAGKTLGRLS SEVAAILRGK HKPTYTPHVD TGDHVIIINA EKIELTGKKL TDKIYYRHTQ HPGGLKSRT ALEMRTNYPE KMLELAIKGM LPKGSLGRQM FKKLNVYRGS EHPHEAQKPE VYELRG

UniProtKB: Large ribosomal subunit protein uL13

Macromolecule #10: 50S ribosomal protein L14

• Macromolecule: Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 13.175288 KDa

Sequence

String:

MIQQETRLKV ADNSGAREVL TIKVLGGSGR KTANIGDVIV CTVKQATPGG VVKKGEVVKA VIVRTKSGAR RSDGSYISFD ENACVIIRD DKSPRGTRIF GPVARELREN NFMKIVSLAP EVI

UniProtKB: Large ribosomal subunit protein uL14

Macromolecule #11: 50S ribosomal protein L15

• Macromolecule: Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 15.410694 KDa

Sequence

String:

MKLHELKPSE GSRKTRNRVG RGIGSGNGKT AGKGHKGQNA RSGGGVRPGF EGGQMPLFQR LPKRGFTNIN RKEYAVVNLD KLNGFAEGT EVTPELLLET GVISKLNAGV KILGNGKLEK KLTVKANKFS ASAKEAVEAA GGTAEVI

UniProtKB: Large ribosomal subunit protein uL15

Macromolecule #12: 50S ribosomal protein L16

• Macromolecule: Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 16.223049 KDa

Sequence

String:

MLLPKRVKYR REHRGKMRGR AKGGTEVHFG EFGIQALEAS WITNRQIEAA RIAMTRYMKR GGKVWIKIFP SKPYTAKPLE VRMGSGKGA PEGWVAVVKP GKVLFEISGV SEEVAREALR LASHKLPIKT KFVKREEIGG ESNES

UniProtKB: Large ribosomal subunit protein uL16

Macromolecule #13: 50S ribosomal protein L17

• Macromolecule: Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 13.774806 KDa

Sequence

String:

MSYRKLGRTS AQRKAMLRDL TTDLIINERI ETTETRAKEL RSVVEKMITL GKRGDLHARR QAAAYIRNEV ANEENNQDAL QKLFSDIAT RYEERQGGYT RIMKLGPRRG DGAPMAIIEL V

UniProtKB: Large ribosomal subunit protein bL17

Macromolecule #14: 50S ribosomal protein L18

• Macromolecule: Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 12.993829 KDa

Sequence

String:

MITKTSKNAA RLKRHARVRA KLSGTAERPR LNVFRSNKHI YAQIIDDVNG VTLASASTLD KDLNVESTGD TSAATKVGEL VAKRAAEKG ISDVVFDRGG YLYHGRVKAL ADAAREAGLK F

UniProtKB: Large ribosomal subunit protein uL18

Macromolecule #16: 50S ribosomal protein L20

• Macromolecule: Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 13.669189 KDa

Sequence

String:

MPRVKGGTVT RKRRKKVLKL AKGYFGSKHT LYKVANQQVM KSGNYAFRDR RQKKRDFRKL WITRINAAAR MNGLSYSRLM HGLKLSGIE VNRKMLADLA VNDLTAFNQL ADAAKAQLNK

UniProtKB: Large ribosomal subunit protein bL20

Macromolecule #17: Rqc2 homolog RqcH

• Macromolecule: Name: Rqc2 homolog RqcH / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 65.307398 KDa

Sequence

String:

MSFDGMFTYG MTHELNEKIM GGRITKIHQP YKHDVIFHIR AKGKNQKLLL SAHPSYSRVH ITAQAYENPS EPPMFCMLLR KHIEGGFIE KIEQAGLDRI MIFHIKSRNE IGDETVRKLY VEIMGRHSNI ILTDAAENVI IDGLKHLSPS MNSYRTVLPG Q DYKLPPAQ DKISPLEASE DDILRHLSFQ EGRLDKQIVD HFSGVSPLFA KEAVHRAGLA NKVTLPKALL ALFAEVKEHR FI PNITTVN GKEYFYLLEL THLKGEARRF DSLSELLDRF YFGKAERDRV KQQAQDLERF VVNERKKNAN KIKKLEKTLE YSE NAKEFQ LYGELLTANL YMLKKGDKQA EVINYYDEES PTITIPLNPN KTPSENAQAY FTKYQKAKNS VAVVEEQIRL AQEE IEYFD QLIQQLSSAS PRDISEIREE LVEGKYLRPK QQKGQKKQKP HNPVLETYES TSGLTILVGK NNRQNEYLTT RVAAR DDIW LHTKDIPGSH VVIRSSEPDE QTIMEAATIA AYFSKAKDSS SVPVDYTKIR HVKKPNGAKP GFVTYDSQHT VFVTPD ADT VIKLKKS

UniProtKB: Rqc2 homolog RqcH

Macromolecule #18: 50S ribosomal protein L22

• Macromolecule: Name: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 12.481608 KDa

Sequence

String:

MQAKAVARTV RIAPRKARLV MDLIRGKQVG EAVSILNLTP RAASPIIEKV LKSAIANAEH NYEMDANNLV ISQAFVDEGP TLKRFRPRA MGRASQINKR TSHITIVVSE KKEG

UniProtKB: Large ribosomal subunit protein uL22

Macromolecule #19: 50S ribosomal protein L24

• Macromolecule: Name: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 11.16612 KDa

Sequence

String:

MHVKKGDKVM VISGKDKGKQ GTILAAFPKK DRVLVEGVNM VKKHSKPTQA NPQGGISNQE APIHVSNVMP LDPKTGEVTR VGYKVEDGK KVRVAKKSGQ VLDK

UniProtKB: Large ribosomal subunit protein uL24

Macromolecule #20: 50S ribosomal protein L27

• Macromolecule: Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis (strain 168) (bacteria)
• Molecular weight: Theoretical: 10.391855 KDa

Sequence

String:

MLRLDLQFFA SKKGVGSTKN GRDSEAKRLG AKRADGQFVT GGSILYRQRG TKIYPGENVG RGGDDTLFAK IDGTVKFERF GRDRKKVSV YPVAQ

UniProtKB: Large ribosomal subunit protein bL27

Macromolecule #21: nascent polyalanine

• Macromolecule: Name: nascent polyalanine / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 515.56 Da

Sequence

String:

AAAAAAA

Macromolecule #22: 50S ribosomal protein L28

• Macromolecule: Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 6.826144 KDa

Sequence

String:

MARKCVITGK KTTAGNNRSH AMNASKRTWG ANLQKVRILV NGKPKKVYVS ARALKSGKVE RV

UniProtKB: Large ribosomal subunit protein bL28

Macromolecule #23: Uncharacterized protein YabO

• Macromolecule: Name: Uncharacterized protein YabO / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 9.737266 KDa

Sequence

String:

MRLDKFLKVS RLIKRRTLAK EVADQGRISI NGNQAKASSD VKPGDELTVR FGQKLVTVQV NELKDTTKKE EAANMYTILK EEKLGE

UniProtKB: RQC P-site tRNA stabilizing factor

Macromolecule #24: 50S ribosomal protein L30

• Macromolecule: Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 6.650795 KDa

Sequence

String:

MAKLEITLKR SVIGRPEDQR VTVRTLGLKK TNQTVVHEDN AAIRGMINKV SHLVSVKEQ

UniProtKB: Large ribosomal subunit protein uL30

Macromolecule #25: 50S ribosomal protein L19

• Macromolecule: Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 13.416853 KDa

Sequence

String:

MQKLIEDITK EQLRTDLPAF RPGDTLRVHV KVVEGNRERI QIFEGVVIKR RGGGISETFT VRKISYGVGV ERTFPVHTPK IAKIEVVRY GKVRRAKLYY LRELRGKAAR IKEIRR

UniProtKB: Large ribosomal subunit protein bL19

Macromolecule #26: 50S ribosomal protein L32

• Macromolecule: Name: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 6.745073 KDa

Sequence

String:

MAVPFRRTSK MKKRLRRTHF KLNVPGMTEC PSCGEMKLSH RVCKACGSYN GKDINVKSN

UniProtKB: Large ribosomal subunit protein bL32

Macromolecule #27: 50S ribosomal protein L33 1

• Macromolecule: Name: 50S ribosomal protein L33 1 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 5.915875 KDa

Sequence

String:

MRVNITLACT ECGERNYISK KNKRNNPDRV EFKKYCPRDK KSTLHRETK

UniProtKB: Large ribosomal subunit protein bL33A

Macromolecule #28: 50S ribosomal protein L34

• Macromolecule: Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 5.271332 KDa

Sequence

String:

MKRTFQPNNR KRSKVHGFRS RMSSKNGRLV LARRRRKGRK VLSA

UniProtKB: Large ribosomal subunit protein bL34

Macromolecule #29: 50S ribosomal protein L35

• Macromolecule: Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 7.581128 KDa

Sequence

String:

MPKMKTHRGS AKRFKKTGSG KLKRSHAYTS HLFANKSQKQ KRKLRKSAVV SAGDFKRIKQ MLANIK

UniProtKB: Large ribosomal subunit protein bL35

Macromolecule #30: 50S ribosomal protein L36

• Macromolecule: Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 4.318422 KDa

Sequence

String:

MKVRPSVKPI CEKCKVIRRK GKVMVICENP KHKQKQG

UniProtKB: Large ribosomal subunit protein bL36

Macromolecule #31: 50S ribosomal protein L21

• Macromolecule: Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 11.296081 KDa

Sequence

String:

MYAIIKTGGK QIKVEEGQTV YIEKLAAEAG ETVTFEDVLF VGGDNVKVGN PTVEGATVTA KVEKQGRAKK ITVFRYKPKK NVHKKQGHR QPYTKVTIEK INA

UniProtKB: Large ribosomal subunit protein bL21

Macromolecule #32: 50S ribosomal protein L23

• Macromolecule: Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 10.978813 KDa

Sequence

String:

MKDPRDVLKR PVITERSADL MTEKKYTFEV DVRANKTEVK DAVESIFGVK VDKVNIMNYK GKSKRVGRYT GMTSRRRKAI VKLTADSKE IEIFEA

UniProtKB: Large ribosomal subunit protein uL23

Macromolecule #33: 50S ribosomal protein L29

• Macromolecule: Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
• Molecular weight: Theoretical: 7.728029 KDa

Sequence

String:

MKANEIRDLT TAEIEQKVKS LKEELFNLRF QLATGQLENT ARIREVRKAI ARMKTVIRER EIAANK

UniProtKB: Large ribosomal subunit protein uL29

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.4
• Grid: Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
• Vitrification: Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Energy filter - Slit width: 20 eV
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
• Sample stage: Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 5869410
• Startup model: Type of model: EMDB MAP
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 138382
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
• Final 3D classification: Software - Name: RELION (ver. 3.0)

Atomic model buiding 1

Initial model

PDB ID	Chain
3j9w	source_name: PDB, initial_model_type: experimental model
5h3x	source_name: PDB, initial_model_type: experimental model
5h3w	source_name: PDB, initial_model_type: experimental model
1dm9	source_name: PDB, initial_model_type: experimental model

Output model

PDB-7aqc:
Structure of the bacterial RQC complex (Decoding State)