8QBT: E. coli ApdP-stalled ribosomal complex

E. coli ApdP-stalled ribosomal complex. Determined by electron microscopy at 2.2 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 2.2 Å
Organisms: Escherichia coli BW25113, Sinorhizobium medicae
Chains: 52
Atoms: 141,132
Mol. weight: 2149.99 kDa
Ligands: ZN, PRO, MG
Released: 20 Mar 2024

Explore 8QBT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QBT contains 216 α-helices and 272 β-strands across 44 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 1: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	13-25	13
β-strand	31-33	3	69
β-strand	39	1	70
α-helix	40-41	2
α-helix	42-44	3
β-strand	48-52	5	69
β-strand	57-61	5	69
α-helix	64-66	3
β-strand	70	1	70
α-helix	71-74	4

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-41	34
α-helix	44-61	18
α-helix	71-86	16

Chain 3: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	25-32	8
β-strand	35	1	51
α-helix	36-37	2
α-helix	39-51	13

Chain a: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	17-19	3
β-strand	29-30	2	84
β-strand	37-38	2	84
β-strand	42	1	55
β-strand	48-49	2	85
β-strand	52-53	2	85

Chain b: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7-13	7	1
β-strand	20-25	6	1
α-helix	33-34	2
β-strand	35-40	6	1
β-strand	45-50	6	1

Chain c: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-22	5
α-helix	25-37	13

Chain C: 10 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	2
α-helix	6-7	2
β-strand	17-19	3	2
β-strand	24	1	3
α-helix	31-33	3
β-strand	34-35	2	4
β-strand	43	1	5
β-strand	49	1	5
β-strand	54	1	6
α-helix	61	1
β-strand	62-63	2	4
β-strand	65	1	3
β-strand	76-82	7	3
β-strand	91-96	6	3
β-strand	101-105	5	3
β-strand	107	1	7
β-strand	115-116	2	3
β-strand	118	1	8
β-strand	129-131	3	8
α-helix	132-134	3
α-helix	136	1
β-strand	140-142	3	8
β-strand	144	1	9
β-strand	154	1	9
β-strand	162-168	7	8
β-strand	171-175	5	8
β-strand	181-185	5	8
β-strand	189-192	4	8
β-strand	195	1	7
α-helix	198-202	5
β-strand	204	1	2
α-helix	208-213	6
β-strand	216	1	6
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	10
β-strand	251	1	10
α-helix	264-266	3
β-strand	267-269	3	8

Chain d: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	11
β-strand	22-24	3	11
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	11
α-helix	50-51	2
α-helix	52-61	10

36 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
23S rRNA	A	RNA	2903	Escherichia coli BW25113
5S rRNA	B	RNA	120	Escherichia coli BW25113
Large ribosomal subunit protein uL2	C	protein	273	Escherichia coli BW25113	P60422 (AlphaFold model)
50S ribosomal protein L3	D	protein	209	Escherichia coli BW25113	P60438 (AlphaFold model)
Large ribosomal subunit protein uL4	E	protein	201	Escherichia coli BW25113	P60723 (AlphaFold model)
Large ribosomal subunit protein uL5	F	protein	179	Escherichia coli BW25113	P62399 (AlphaFold model)
Large ribosomal subunit protein uL6	G	protein	177	Escherichia coli BW25113	P0AG55
Large ribosomal subunit protein bL9	H	protein	149	Escherichia coli BW25113	P0A7R1
Large ribosomal subunit protein uL13	J	protein	142	Escherichia coli BW25113	P0AA10
Large ribosomal subunit protein uL14	K	protein	123	Escherichia coli BW25113	P0ADY3
50S ribosomal protein L15	L	protein	144	Escherichia coli BW25113	P02413
50S ribosomal protein L16	M	protein	136	Escherichia coli BW25113	P0ADY7

39 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8QBT_1 23S rRNA (chains A)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCCUAAUCGGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU

Sequence of entity 2 (B), FASTA

>8QBT_2 5S rRNA (chains B)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU

Sequence of entity 3 (C), FASTA

>8QBT_3 Large ribosomal subunit protein uL2 (chains C)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 4 (D), FASTA

>8QBT_4 50S ribosomal protein L3 (chains D)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 5 (E), FASTA

>8QBT_5 Large ribosomal subunit protein uL4 (chains E)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 6 (F), FASTA

>8QBT_6 Large ribosomal subunit protein uL5 (chains F)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Sequence of entity 7 (G), FASTA

>8QBT_7 Large ribosomal subunit protein uL6 (chains G)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 8 (H), FASTA

>8QBT_8 Large ribosomal subunit protein bL9 (chains H)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Sequence of entity 9 (J), FASTA

>8QBT_9 Large ribosomal subunit protein uL13 (chains J)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI

Sequence of entity 10 (K), FASTA

>8QBT_10 Large ribosomal subunit protein uL14 (chains K)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EVL

Sequence of entity 11 (L), FASTA

>8QBT_11 50S ribosomal protein L15 (chains L)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 12 (M), FASTA

>8QBT_12 50S ribosomal protein L16 (chains M)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
PRO	Proline	C5 H9 N O2	1
MG	Magnesium ion	Mg	248

Water and common crystallization additives (K) are not listed.

Primary citation

RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Morici, M., Gabrielli, S., Fujiwara, K. et al. Nat Commun (2024) 15:2432-2432. DOI 10.1038/s41467-024-46761-3 · PubMed

Other PDB entries of the same protein (UniProt P60422 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
8CGV 1.66 Å, Tiamulin bound to the 50S subunit
8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
8CAM 1.86 Å, Evernimicin bound to the 50S subunit
9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
8E30 1.91 Å, E. coli 50S ribosome bound to compound streptogramin A analog 3142

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