7AQD: Bacterial RQC complex
Structure of the bacterial RQC complex (Translocating State). Determined by electron microscopy at 3.1 Å resolution. Released 25 Nov 2020.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Bacillus subtilis subsp. subtilis str. 168
- Chains
- 32
- Atoms
- 94,357
- Mol. weight
- 1425.45 kDa
- Released
- 25 Nov 2020
Explore 7AQD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7AQD contains 133 α-helices and 206 β-strands across 28 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain a: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| α-helix | 21-22 | 2 | |
| β-strand | 28-34 | 7 | 38 |
| β-strand | 43-54 | 12 | 38 |
| α-helix | 57-59 | 3 | |
| β-strand | 61-68 | 8 | 38 |
| β-strand | 71-78 | 8 | 38 |
| β-strand | 84-91 | 8 | 38 |
| β-strand | 93-94 | 2 | 63 |
| α-helix | 101-104 | 4 | |
| α-helix | 109-112 | 4 | |
| β-strand | 116-117 | 2 | 63 |
Chain b: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 10-16 | 7 | |
| α-helix | 23-25 | 3 | |
| β-strand | 27-28 | 2 | 64 |
| β-strand | 37-38 | 2 | 64 |
| β-strand | 48-49 | 2 | 65 |
| β-strand | 52-53 | 2 | 65 |
Chain c: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-9 | 8 | 66 |
| β-strand | 15-22 | 8 | 66 |
| α-helix | 29-30 | 2 | |
| β-strand | 31-36 | 6 | 66 |
| β-strand | 41-47 | 7 | 66 |
Chain C: 8 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 7 |
| α-helix | 6-7 | 2 | |
| β-strand | 17-19 | 3 | 7 |
| α-helix | 31-33 | 3 | |
| β-strand | 34-36 | 3 | 8 |
| β-strand | 43 | 1 | 9 |
| β-strand | 49 | 1 | 9 |
| β-strand | 54 | 1 | 10 |
| β-strand | 61-63 | 3 | 8 |
| β-strand | 65 | 1 | 11 |
| β-strand | 76-82 | 7 | 11 |
| β-strand | 91-96 | 6 | 11 |
| β-strand | 101-105 | 5 | 11 |
| β-strand | 107 | 1 | 12 |
| β-strand | 115-116 | 2 | 11 |
| β-strand | 129-131 | 3 | 13 |
| α-helix | 136 | 1 | |
| β-strand | 140 | 1 | 14 |
| β-strand | 141-142 | 2 | 13 |
| β-strand | 163-167 | 5 | 14 |
| β-strand | 171-175 | 5 | 14 |
| α-helix | 177-179 | 3 | |
| β-strand | 181-185 | 5 | 14 |
| β-strand | 189-192 | 4 | 13 |
| β-strand | 195 | 1 | 12 |
| α-helix | 198-202 | 5 | |
| α-helix | 208-213 | 6 | |
| β-strand | 216 | 1 | 10 |
| α-helix | 222-224 | 3 | |
| β-strand | 247 | 1 | 15 |
| β-strand | 253 | 1 | 15 |
| α-helix | 265-268 | 4 | |
| β-strand | 270-272 | 3 | 14 |
Chain d: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-15 | 7 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-37 | 13 | |
Chain D: 7 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-16 | 13 | 19 |
| β-strand | 22-29 | 8 | 19 |
| β-strand | 33-39 | 7 | 20 |
| β-strand | 48-55 | 8 | 20 |
| α-helix | 63-68 | 6 | |
| β-strand | 77-83 | 7 | 20 |
| α-helix | 95 | 1 | |
| β-strand | 96-97 | 2 | 20 |
| α-helix | 99-101 | 3 | |
| β-strand | 107-113 | 7 | 19 |
| α-helix | 114-116 | 3 | |
| β-strand | 118-120 | 3 | 21 |
| α-helix | 122-126 | 5 | |
| α-helix | 128-132 | 5 | |
| α-helix | 154-155 | 2 | |
| β-strand | 162-164 | 3 | 21 |
| β-strand | 168-180 | 13 | 19 |
| β-strand | 185-189 | 5 | 19 |
| β-strand | 199-204 | 6 | 19 |
Chain e: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-13 | 6 | |
| β-strand | 15 | 1 | 5 |
| β-strand | 23-25 | 3 | 5 |
| α-helix | 38-44 | 7 | |
| β-strand | 47-49 | 3 | 5 |
| α-helix | 52-58 | 7 | |
Chain E: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 24 |
| β-strand | 6-7 | 2 | 25 |
| β-strand | 16-18 | 3 | 24 |
| α-helix | 21-24 | 4 | |
| α-helix | 27-28 | 2 | |
| α-helix | 30-41 | 12 | |
| α-helix | 103-119 | 17 | |
| β-strand | 123-126 | 4 | 25 |
| α-helix | 136-145 | 10 | |
| β-strand | 152-156 | 5 | 25 |
| α-helix | 161-165 | 5 | |
| β-strand | 173-177 | 5 | 25 |
| α-helix | 183-189 | 7 | |
| β-strand | 192-194 | 3 | 25 |
| α-helix | 196-205 | 10 | |
20 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Rqc2 homolog RqcH | R | protein | 570 | Bacillus subtilis subsp. subtilis str. 168 | O34693 (AlphaFold model) |
| 23S ribosomal RNA | A | RNA | 2918 | Bacillus subtilis subsp. subtilis str. 168 | |
| 5S ribosomal RNA | B | RNA | 112 | Bacillus subtilis subsp. subtilis str. 168 | |
| 50S ribosomal protein L2 | C | protein | 277 | Bacillus subtilis subsp. subtilis str. 168 | P42919 (AlphaFold model) |
| 50S ribosomal protein L3 | D | protein | 209 | Bacillus subtilis subsp. subtilis str. 168 | P42920 (AlphaFold model) |
| 50S ribosomal protein L4 | E | protein | 207 | Bacillus subtilis subsp. subtilis str. 168 | P42921 (AlphaFold model) |
| 50S ribosomal protein L5 | F | protein | 179 | Bacillus subtilis subsp. subtilis str. 168 | P12877 |
| 50S ribosomal protein L6 | G | protein | 179 | Bacillus subtilis subsp. subtilis str. 168 | P46898 |
| 50S ribosomal protein L11 | I | protein | 141 | Bacillus subtilis subsp. subtilis str. 168 | Q06796 |
| 50S ribosomal protein L13 | J | protein | 145 | Bacillus subtilis subsp. subtilis str. 168 | P70974 |
| 50S ribosomal protein L14 | K | protein | 122 | Bacillus subtilis subsp. subtilis str. 168 | P12875 |
| 50S ribosomal protein L15 | L | protein | 146 | Bacillus subtilis subsp. subtilis str. 168 | P19946 |
20 more molecules are not listed.
Sequence of entity 1 (R), FASTA
>7AQD_1 Rqc2 homolog RqcH (chains R)
MSFDGMFTYGMTHELNEKIMGGRITKIHQPYKHDVIFHIRAKGKNQKLLLSAHPSYSRVH
ITAQAYENPSEPPMFCMLLRKHIEGGFIEKIEQAGLDRIMIFHIKSRNEIGDETVRKLYV
EIMGRHSNIILTDAAENVIIDGLKHLSPSMNSYRTVLPGQDYKLPPAQDKISPLEASEDD
ILRHLSFQEGRLDKQIVDHFSGVSPLFAKEAVHRAGLANKVTLPKALLALFAEVKEHRFI
PNITTVNGKEYFYLLELTHLKGEARRFDSLSELLDRFYFGKAERDRVKQQAQDLERFVVN
ERKKNANKIKKLEKTLEYSENAKEFQLYGELLTANLYMLKKGDKQAEVINYYDEESPTIT
IPLNPNKTPSENAQAYFTKYQKAKNSVAVVEEQIRLAQEEIEYFDQLIQQLSSASPRDIS
EIREELVEGKYLRPKQQKGQKKQKPHNPVLETYESTSGLTILVGKNNRQNEYLTTRVAAR
DDIWLHTKDIPGSHVVIRSSEPDEQTIMEAATIAAYFSKAKDSSSVPVDYTKIRHVKKPN
GAKPGFVTYDSQHTVFVTPDADTVIKLKKS
Sequence of entity 2 (A), FASTA
>7AQD_2 23S ribosomal RNA (chains A)
UUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGGAC
GAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUGGG
GAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAGGC
AGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCCCU
GAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUGUA
GGACACUCUGUACGGAGUUACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCCGC
CAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCUCUCCUGAGUGGAUCCUGAGUAC
GGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUACUC
CCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGG
AGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGAUG
GCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCUCGUGCAAGGUUAAGCAGAAGAU
GCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGACCCGA
AACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCGAA
CCCACGCACGUUGAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGAAC
CUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGUCUUG
GAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAACUCC
GAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAAAG
GGAAACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUGUG
GAGUUGCUUAGACAACCAGGAUGUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGUAA
UAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGGCUAAACGUAUCACCGAA
GCUGCGGACUGUUCUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGACC
GGAAGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGGUG
AGAAUCCCCUCCACCGAAUGCCUAAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUUAG
UCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAACAGGUUGAUAUUCCUGUA
CCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAUUG
GAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGCCUGA
GCUGUGAUGGCGAGCGAAAUAUAGUAGCGAAGUUCCUGAUUCCACACUGCCAAGAAAAGC
CUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAGAAUC
CUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGG
AGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGCGA
CUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACGCC
UGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGAAGCC
CCAGUAAACGGCGGCCGUAAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCC
GACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUUA
UAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAGCUUUAC
UGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCCUUGGAAACC
GGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGACCUUCUA
ACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGGGGCGGUC
GCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCG
CAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGACGAAA
GUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCU
ACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGUUUGGCAC
CUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGC
CCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCG
UCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACGC
ACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCGGACGGGA
UAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAUUCCGCAA
GGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGUGGCGACA
CAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAAC
Sequence of entity 3 (B), FASTA
>7AQD_3 5S ribosomal RNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA
Sequence of entity 4 (C), FASTA
>7AQD_4 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 5 (D), FASTA
>7AQD_5 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 6 (E), FASTA
>7AQD_6 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Sequence of entity 7 (F), FASTA
>7AQD_7 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK
Sequence of entity 8 (G), FASTA
>7AQD_8 50S ribosomal protein L6 (chains G)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK
Sequence of entity 9 (I), FASTA
>7AQD_9 50S ribosomal protein L11 (chains I)
MAKKVVKVVKLQIPAGKANPAPPVGPALGQAGVNIMGFCKEFNARTADQAGLIIPVEISV
YEDRSFTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATVKRDKVREIAETKMPDLNAAD
VEAAMRMVEGTARSMGIVIED
Sequence of entity 10 (J), FASTA
>7AQD_10 50S ribosomal protein L13 (chains J)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG
Sequence of entity 11 (K), FASTA
>7AQD_11 50S ribosomal protein L14 (chains K)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI
Sequence of entity 12 (L), FASTA
>7AQD_12 50S ribosomal protein L15 (chains L)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI
Primary citation
Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC. Filbeck, S., Cerullo, F., Paternoga, H. et al. Mol Cell (2021) 81:104. DOI 10.1016/j.molcel.2020.11.001 · PubMed
Other PDB entries of the same protein (UniProt O34693 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7AS8 2.9 Å, Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with…
- 7AQC 2.99 Å, Structure of the bacterial RQC complex (Decoding State)
- 7OPE 3.2 Å, RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)
- 8S1U 3.4 Å, YlmH bound to stalled 50S subunits with RqcH and PtRNA
- 7AS9 3.5 Å, Bacillus subtilis ribosome-associated quality control complex state A. Ribosomal 50S…
- 7ASA 3.5 Å, Bacillus subtilis ribosome-associated quality control complex state B, multibody…
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