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- EMDB-11864: Structure of the bacterial RQC complex (Translocating State) -

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Basic information

Entry
Database: EMDB / ID: EMD-11864
TitleStructure of the bacterial RQC complex (Translocating State)
Map data
Sample
  • Complex: Bacterial RQC complex
    • Protein or peptide: x 29 types
    • RNA: x 3 types
KeywordsRIBOSOME / rqch / rqc / rqc2 / hsp15 / fibronectin-binding protein / NEMF / ribosome-associated quality control / ribosome-associated / 50s / Alanine-tailing
Function / homology
Function and homology information


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 ...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 / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / DNA binding / RNA binding / cytoplasm
Similarity search - Function
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. ...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 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 L17 signature. / 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 L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, 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 L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / 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 L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / 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
Similarity search - Domain/homology
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 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 / 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
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFilbeck S / Pfeffer S
Funding support Germany, United States, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1036 Germany
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS102414 United States
CitationJournal: 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 ...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
DepositionOct 21, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7aqd
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11864.png

Downloads & links

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Map

FileDownload / File: emd_11864.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0085 / Movie #1: 0.01
Minimum - Maximum-0.07061839 - 0.17702931
Average (Standard dev.)0.0002351541 (±0.006163751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z410.880410.880410.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0710.1770.000

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Supplemental data

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Sample components

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Entire : Bacterial RQC complex

EntireName: Bacterial RQC complex
Components
  • Complex: Bacterial RQC complex
    • Protein or peptide: Rqc2 homolog RqcH
    • 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
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L22
    • RNA: Ala-tRNA (A/P-site)
    • 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: 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

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Supramolecule #1: Bacterial RQC complex

SupramoleculeName: Bacterial RQC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Macromolecule #1: Rqc2 homolog RqcH

MacromoleculeName: Rqc2 homolog RqcH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 65.307398 KDa
SequenceString: MSFDGMFTYG MTHELNEKIM GGRITKIHQP YKHDVIFHIR AKGKNQKLLL SAHPSYSRVH ITAQAYENPS EPPMFCMLLR KHIEGGFIE KIEQAGLDRI MIFHIKSRNE IGDETVRKLY VEIMGRHSNI ILTDAAENVI IDGLKHLSPS MNSYRTVLPG Q DYKLPPAQ ...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

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Macromolecule #4: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 30.335125 KDa
SequenceString: MAIKKYKPTS NGRRGMTTSD FAEITTDKPE KSLLAPLHKK GGRNNQGKLT VRHQGGGHKR QYRVIDFKRD KDGIPGRVAT VEYDPNRSA NIALINYADG EKRYILAPKG IQVGTEIMSG PEADIKVGNA LPLINIPVGT VVHNIELKPG KGGQLVRSAG T SAQVLGKE ...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

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Macromolecule #5: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 22.723348 KDa
SequenceString: MTKGILGRKI GMTQVFAENG DLIPVTVIEA APNVVLQKKT AENDGYEAIQ LGFDDKREKL SNKPEKGHVA KAETAPKRFV KELRGVEMD AYEVGQEVKV EIFSAGEIVD VTGVSKGKGF QGAIKRHGQS RGPMSHGSRY HRRPGSMGPV DPNRVFKGKL L PGRMGGEQ ...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

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Macromolecule #6: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 22.424951 KDa
SequenceString: MPKVALYNQN GSTAGDIELN ASVFGIEPNE SVVFDAILMQ RASLRQGTHK VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVV FGPTPRSYSY KLPKKVRRLA IKSVLSSKVI DNNIIVLEDL TLDTAKTKEM AAILKGLSVE KKALIVTADA N EAVALSAR ...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

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Macromolecule #7: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 20.177564 KDa
SequenceString:
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

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Macromolecule #8: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 19.543389 KDa
SequenceString:
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

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Macromolecule #9: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 14.951442 KDa
SequenceString:
MAKKVVKVVK LQIPAGKANP APPVGPALGQ AGVNIMGFCK EFNARTADQA GLIIPVEISV YEDRSFTFIT KTPPAAVLLK KAAGIESGS GEPNRNKVAT VKRDKVREIA ETKMPDLNAA DVEAAMRMVE GTARSMGIVI ED

UniProtKB: Large ribosomal subunit protein uL11

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Macromolecule #10: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 16.407104 KDa
SequenceString:
MRTTPMANAS TIERKWLVVD AAGKTLGRLS SEVAAILRGK HKPTYTPHVD TGDHVIIINA EKIELTGKKL TDKIYYRHTQ HPGGLKSRT ALEMRTNYPE KMLELAIKGM LPKGSLGRQM FKKLNVYRGS EHPHEAQKPE VYELRG

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #11: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 13.175288 KDa
SequenceString:
MIQQETRLKV ADNSGAREVL TIKVLGGSGR KTANIGDVIV CTVKQATPGG VVKKGEVVKA VIVRTKSGAR RSDGSYISFD ENACVIIRD DKSPRGTRIF GPVARELREN NFMKIVSLAP EVI

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #12: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 15.410694 KDa
SequenceString:
MKLHELKPSE GSRKTRNRVG RGIGSGNGKT AGKGHKGQNA RSGGGVRPGF EGGQMPLFQR LPKRGFTNIN RKEYAVVNLD KLNGFAEGT EVTPELLLET GVISKLNAGV KILGNGKLEK KLTVKANKFS ASAKEAVEAA GGTAEVI

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #13: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 16.223049 KDa
SequenceString:
MLLPKRVKYR REHRGKMRGR AKGGTEVHFG EFGIQALEAS WITNRQIEAA RIAMTRYMKR GGKVWIKIFP SKPYTAKPLE VRMGSGKGA PEGWVAVVKP GKVLFEISGV SEEVAREALR LASHKLPIKT KFVKREEIGG ESNES

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #14: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 13.774806 KDa
SequenceString:
MSYRKLGRTS AQRKAMLRDL TTDLIINERI ETTETRAKEL RSVVEKMITL GKRGDLHARR QAAAYIRNEV ANEENNQDAL QKLFSDIAT RYEERQGGYT RIMKLGPRRG DGAPMAIIEL V

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #15: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 12.993829 KDa
SequenceString:
MITKTSKNAA RLKRHARVRA KLSGTAERPR LNVFRSNKHI YAQIIDDVNG VTLASASTLD KDLNVESTGD TSAATKVGEL VAKRAAEKG ISDVVFDRGG YLYHGRVKAL ADAAREAGLK F

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #16: 50S ribosomal protein L20

MacromoleculeName: 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 weightTheoretical: 13.669189 KDa
SequenceString:
MPRVKGGTVT RKRRKKVLKL AKGYFGSKHT LYKVANQQVM KSGNYAFRDR RQKKRDFRKL WITRINAAAR MNGLSYSRLM HGLKLSGIE VNRKMLADLA VNDLTAFNQL ADAAKAQLNK

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #17: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 12.481608 KDa
SequenceString:
MQAKAVARTV RIAPRKARLV MDLIRGKQVG EAVSILNLTP RAASPIIEKV LKSAIANAEH NYEMDANNLV ISQAFVDEGP TLKRFRPRA MGRASQINKR TSHITIVVSE KKEG

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #19: 50S ribosomal protein L24

MacromoleculeName: 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 weightTheoretical: 11.16612 KDa
SequenceString:
MHVKKGDKVM VISGKDKGKQ GTILAAFPKK DRVLVEGVNM VKKHSKPTQA NPQGGISNQE APIHVSNVMP LDPKTGEVTR VGYKVEDGK KVRVAKKSGQ VLDK

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #20: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 10.391855 KDa
SequenceString:
MLRLDLQFFA SKKGVGSTKN GRDSEAKRLG AKRADGQFVT GGSILYRQRG TKIYPGENVG RGGDDTLFAK IDGTVKFERF GRDRKKVSV YPVAQ

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #21: nascent polyalanine

MacromoleculeName: 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 weightTheoretical: 515.56 Da
SequenceString:
AAAAAAA

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Macromolecule #22: 50S ribosomal protein L28

MacromoleculeName: 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 weightTheoretical: 6.826144 KDa
SequenceString:
MARKCVITGK KTTAGNNRSH AMNASKRTWG ANLQKVRILV NGKPKKVYVS ARALKSGKVE RV

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #23: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 6.650795 KDa
SequenceString:
MAKLEITLKR SVIGRPEDQR VTVRTLGLKK TNQTVVHEDN AAIRGMINKV SHLVSVKEQ

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #24: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 13.416853 KDa
SequenceString:
MQKLIEDITK EQLRTDLPAF RPGDTLRVHV KVVEGNRERI QIFEGVVIKR RGGGISETFT VRKISYGVGV ERTFPVHTPK IAKIEVVRY GKVRRAKLYY LRELRGKAAR IKEIRR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #25: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 6.745073 KDa
SequenceString:
MAVPFRRTSK MKKRLRRTHF KLNVPGMTEC PSCGEMKLSH RVCKACGSYN GKDINVKSN

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #26: 50S ribosomal protein L33 1

MacromoleculeName: 50S ribosomal protein L33 1 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 5.915875 KDa
SequenceString:
MRVNITLACT ECGERNYISK KNKRNNPDRV EFKKYCPRDK KSTLHRETK

UniProtKB: Large ribosomal subunit protein bL33A

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Macromolecule #27: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 5.271332 KDa
SequenceString:
MKRTFQPNNR KRSKVHGFRS RMSSKNGRLV LARRRRKGRK VLSA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #28: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 7.581128 KDa
SequenceString:
MPKMKTHRGS AKRFKKTGSG KLKRSHAYTS HLFANKSQKQ KRKLRKSAVV SAGDFKRIKQ MLANIK

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #29: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 4.318422 KDa
SequenceString:
MKVRPSVKPI CEKCKVIRRK GKVMVICENP KHKQKQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #30: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 11.296081 KDa
SequenceString:
MYAIIKTGGK QIKVEEGQTV YIEKLAAEAG ETVTFEDVLF VGGDNVKVGN PTVEGATVTA KVEKQGRAKK ITVFRYKPKK NVHKKQGHR QPYTKVTIEK INA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #31: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 10.978813 KDa
SequenceString:
MKDPRDVLKR PVITERSADL MTEKKYTFEV DVRANKTEVK DAVESIFGVK VDKVNIMNYK GKSKRVGRYT GMTSRRRKAI VKLTADSKE IEIFEA

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #32: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 7.728029 KDa
SequenceString:
MKANEIRDLT TAEIEQKVKS LKEELFNLRF QLATGQLENT ARIREVRKAI ARMKTVIRER EIAANK

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #2: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 946.39925 KDa
SequenceString: UUAAGUUAGA AAGGGCGCAC GGUGGAUGCC UUGGCACUAG GAGCCGAUGA AGGACGGGAC GAACACCGAU AUGCUUCGGG GAGCUGUAA GCAAGCUUUG AUCCGGAGAU UUCCGAAUGG GGAAACCCAC CACUCGUAAU GGAGUGGUAU CCAUAUCUGA A UUCAUAGG ...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 GAAUGUUGGU ACAGCUUGUA CAGGAUAGGU AGGAGCCUUG GAAACC GGA GCGCCAGCUU CGGUGGAGGC AUCGGUGGGA UACUACCCUG GCUGUAUUGA CCUUCUAACC CGCCGCCCUU AUCGGGC GG GGAGACAGUG UCAGGUGGGC AGUUUGACUG GGGCGGUCGC CUCCUAAAAG GUAACGGAGG CGCCCAAAGG UUCCCUCA G AAUGGUUGGA AAUCAUUCGC AGAGUGUAAA GGCACAAGGG AGCUUGACUG CGAGACCUAC AAGUCGAGCA GGGACGAAA GUCGGGCUUA GUGAUCCGGU GGUUCCGCAU GGAAGGGCCA UCGCUCAACG GAUAAAAGCU ACCCCGGGGA UAACAGGCUU AUCUCCCCC AAGAGUCCAC AUCGACGGGG AGGUUUGGCA CCUCGAUGUC GGCUCAUCGC AUCCUGGGGC UGUAGUCGGU C CCAAGGGU UGGGCUGUUC GCCCAUUAAA GCGGUACGCG AGCUGGGUUC AGAACGUCGU GAGACAGUUC GGUCCCUAUC CG UCGCGGG CGCAGGAAAU UUGAGAGGAG CUGUCCUUAG UACGAGAGGA CCGGGAUGGA CGCACCGCUG GUGUACCAGU UGU UCUGCC AAGGGCAUCG CUGGGUAGCU AUGUGCGGAC GGGAUAAGUG CUGAAAGCAU CUAAGCAUGA AGCCCCCCUC AAGA UGAGA UUUCCCAUUC CGCAAGGAAG UAAGAUCCCU GAAAGAUGAU CAGGUUGAUA GGUCUGAGGU GGAAGUGUGG CGACA CAUG GAGCUGACAG AUACUAAUCG AUCGAGGACU UAAC

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Macromolecule #3: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 36.15752 KDa
SequenceString:
UGGUGGCGAU AGCGAAGAGG UCACACCCGU UCCCAUACCG AACACGGAAG UUAAGCUCUU CAGCGCCGAU GGUAGUCGGG GGUUUCCCC CUGUGAGAGU AGGACGCCGC CAA

GENBANK: GENBANK: CP019662.1

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Macromolecule #18: Ala-tRNA (A/P-site)

MacromoleculeName: Ala-tRNA (A/P-site) / type: rna / ID: 18 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 24.491547 KDa
SequenceString:
GGGGCCUUAG CUCAGCUGGG AGAGCGCCUG CUUUGCACGC AGGAGGUCAG CGGUUCGAUC CCGCUAGGCU CCACCA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5869410
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 24348
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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Atomic model buiding 1

Initial model
PDB IDChain

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
Output model

PDB-7aqd:
Structure of the bacterial RQC complex (Translocating State)

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