8AGZ: 60S ribosomal protein L15-A

Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position. Determined by electron microscopy at 2.6 Å resolution. Released 8 Mar 2023.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 54
Atoms: 151,339
Mol. weight: 2401.27 kDa
Ligands: MG, ZN, SPD
Released: 8 Mar 2023

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

Secondary structure: helices and β-sheets

8AGZ contains 473 α-helices and 391 β-strands across 49 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 0: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-21	18
β-strand	24-29	6	5
α-helix	35-44	10
β-strand	49-53	5	5
α-helix	56-65	10
α-helix	71-75	5
α-helix	76-79	4
β-strand	85-89	5	5
α-helix	94-102	9
β-strand	186-192	7	5
β-strand	195-197	3	5

Chain 1: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	50-52	3

Chain a: 37 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	25-31	7	87
β-strand	38-45	8	87
β-strand	48-55	8	87
β-strand	59-63	5	87
β-strand	65	1	88
α-helix	75-83	9
β-strand	88	1	87
β-strand	89-94	6	89
β-strand	100-105	6	89
β-strand	110-115	6	89
β-strand	122-125	4	89
β-strand	130	1	90
β-strand	131-134	4	89
β-strand	138	1	91
β-strand	143	1	91
β-strand	148	1	90
α-helix	154-158	5
α-helix	162-173	12
α-helix	178-204	27
α-helix	220-227	8
α-helix	233-242	10
α-helix	251-256	6
α-helix	258-277	20
β-strand	282-289	8	92
α-helix	290	1
α-helix	300-303	4
β-strand	304-310	7	92
α-helix	313-315	3
α-helix	318-323	6
β-strand	324-330	7	92
α-helix	334-394	61
α-helix	396-410	15
α-helix	416-428	13
α-helix	432-435	4
β-strand	437	1	93
β-strand	442	1	93
α-helix	443-445	3
β-strand	447-453	7	93
β-strand	503-509	7	93
α-helix	514-560	47
β-strand	567	1	88
α-helix	568-572	5
β-strand	578-581	4	94
β-strand	587-590	4	94
α-helix	594-603	10
β-strand	610-613	4	94
β-strand	620-622	3	94
α-helix	629-631	3
α-helix	632-645	14
α-helix	648-651	4
β-strand	658-661	4	94
β-strand	665-666	2	95
α-helix	670-672	3
α-helix	675-677	3
β-strand	682-683	2	95
β-strand	690-691	2	94
α-helix	692-694	3
β-strand	699-707	9	96
α-helix	841-850	10
α-helix	856-866	11
α-helix	868-904	37
α-helix	905-907	3
α-helix	917-923	7
β-strand	924-925	2	96
α-helix	932-933	2
β-strand	934-943	10	96
α-helix	944-947	4
β-strand	952-957	6	96
α-helix	963-975	13
β-strand	979	1	97
β-strand	989	1	97
α-helix	991-999	9
α-helix	1002-1008	7
β-strand	1015-1016	2	96

Chain A: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
α-helix	17-31	15
β-strand	36-39	4	1
α-helix	45-51	7
β-strand	59-67	9	1
α-helix	76-78	3
α-helix	84-86	3
α-helix	98-109	12
β-strand	114-123	10	1
β-strand	127-135	9	1
α-helix	140-143	4
α-helix	149-152	4
α-helix	154-156	3
α-helix	159-162	4
α-helix	166-172	7
α-helix	178-180	3
α-helix	187-195	9
β-strand	197-199	3	2

Chain b: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	3
β-strand	7-12	6	4
β-strand	19-27	9	4
α-helix	32-34	3
α-helix	38-47	10
β-strand	67-74	8	4
β-strand	80-87	8	4
β-strand	92	1	3

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	6
β-strand	14	1	7
β-strand	15	1	8
α-helix	16-29	14
β-strand	32-36	5	6
α-helix	38-40	3
β-strand	42-44	3	8
α-helix	47-58	12
α-helix	66-68	3
α-helix	76-85	10
α-helix	93-99	7
β-strand	102-104	3	6
β-strand	118	1	6
β-strand	119	1	9
β-strand	124	1	7
α-helix	125-128	4
α-helix	130	1
β-strand	131	1	10
β-strand	133	1	10
β-strand	135-137	3	8
α-helix	138-145	8
α-helix	150-184	35
α-helix	189-196	8

Chain c: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	20-34	15
β-strand	37	1	11
β-strand	47-51	5	11
β-strand	54-57	4	11
β-strand	63-65	3	11
α-helix	74-91	18

Chain C: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	14-22	9	12
α-helix	26-36	11
β-strand	40	1	12
α-helix	41-52	12
β-strand	58-59	2	13
α-helix	67-68	2
β-strand	69	1	14
α-helix	71-73	3
β-strand	80	1	14
β-strand	81-82	2	13
α-helix	85-105	21
β-strand	112-121	10	12
α-helix	122-124	3
β-strand	125-131	7	15
β-strand	135-141	7	15
β-strand	144-152	9	12
α-helix	170-182	13

41 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
60S ribosomal protein L15-A	A	protein	204	Saccharomyces cerevisiae	P05748 (AlphaFold model)
60S ribosomal protein L16-A	B	protein	199	Saccharomyces cerevisiae	P26784 (AlphaFold model)
60S ribosomal protein L17-A	C	protein	184	Saccharomyces cerevisiae	P05740 (AlphaFold model)
60S ribosomal protein L18-A	D	protein	186	Saccharomyces cerevisiae	P0CX49 (AlphaFold model)
60S ribosomal protein L19-A	E	protein	189	Saccharomyces cerevisiae	P0CX82
60S ribosomal protein L20-A	F	protein	172	Saccharomyces cerevisiae	P0CX23
60S ribosomal protein L21-A	G	protein	160	Saccharomyces cerevisiae	Q02753
60S ribosomal protein L22-A	H	protein	121	Saccharomyces cerevisiae	P05749
60S ribosomal protein L23-A	I	protein	137	Saccharomyces cerevisiae	P0CX41
60S ribosomal protein L24-A	J	protein	155	Saccharomyces cerevisiae	P04449
60S ribosomal protein L25	K	protein	142	Saccharomyces cerevisiae	P04456
60S ribosomal protein L26-A	L	protein	127	Saccharomyces cerevisiae	P05743

41 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8AGZ_1 60S ribosomal protein L15-A (chains A)
MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFV
IYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYW
VNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKF
NNTKAGRRKTWKRQNTLSLWRYRK

Sequence of entity 2 (B), FASTA

>8AGZ_2 60S ribosomal protein L16-A (chains B)
MSVEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRK
ATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVV
PQALRVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVAS
ANATAAESDVAKQLAALGY

Sequence of entity 3 (C), FASTA

>8AGZ_3 60S ribosomal protein L17-A (chains C)
MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF
RRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN
QAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQK
RIAA

Sequence of entity 4 (D), FASTA

>8AGZ_4 60S ribosomal protein L18-A (chains D)
MGIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRP
PVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGE
CITLDQLAVRAPKGQNTLILRGPRNSREAVRHFGMGPHKGKAPRILSTGRKFERARGRRR
SKGFKV

Sequence of entity 5 (E), FASTA

>8AGZ_5 60S ribosomal protein L19-A (chains E)
MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSK
SRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLY
HVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEK
RDALLKEDA

Sequence of entity 6 (F), FASTA

>8AGZ_6 60S ribosomal protein L20-A (chains F)
MAHFKEYQVIGRRLPTESVPEPKLFRMRIFASNEVIAKSRYWYFLQKLHKVKKASGEIVS
INQINEAHPTKVKNFGVWVRYDSRSGTHNMYKEIRDVSRVAAVETLYQDMAARHRARFRS
IHILKVAEIEKTADVKRQYVKQFLTKDLKFPLPHRVQKSTKTFSYKRPSTFY

Sequence of entity 7 (G), FASTA

>8AGZ_7 60S ribosomal protein L21-A (chains G)
MGKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGK
TGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKCRQEFLERVKANAAKRAEAK
AQGVAVQLKRQPAQPRESRIVSTEGNVPQTLAPVPYETFI

Sequence of entity 8 (H), FASTA

>8AGZ_8 60S ribosomal protein L22-A (chains H)
MAPNTSRKQKIAKTFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDG
TVVTVVSTAKFSGKYLKYLTKKYLKKNQLRDWIRFVSTKTNEYRLAFYQVTPEEDEEEDE
E

Sequence of entity 9 (I), FASTA

>8AGZ_9 60S ribosomal protein L23-A (chains I)
MSGNGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMA
TVKKGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGK
ECADLWPRVASNSGVVV

Sequence of entity 10 (J), FASTA

>8AGZ_10 60S ribosomal protein L24-A (chains J)
MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIAWTVLFRKHHK
KGITEEVAKKRSRKTVKAQRPITGASLDLIKERRSLKPEVRKANREEKLKANKEKKKAEK
AARKAEKAKSAGTQSSKFSKQQAKGAFQKVAATSR

Sequence of entity 11 (K), FASTA

>8AGZ_11 60S ribosomal protein L25 (chains K)
MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSY
KVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI

Sequence of entity 12 (L), FASTA

>8AGZ_12 60S ribosomal protein L26-A (chains L)
MAKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVR
GSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQ
RKGGKLE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	13
ZN	Zinc ion	Zn	7
SPD	Spermidine	C7 H19 N3	1

Primary citation

Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control. Tesina, P., Ebine, S., Buschauer, R. et al. Mol Cell (2023) 83:607-621.e4. DOI 10.1016/j.molcel.2023.01.020 · PubMed

Other PDB entries of the same protein (UniProt P05748 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
8P8N 2.15 Å, Mouse RPL39 integrated into the yeast 60S ribosomal subunit
8PFR 2.15 Å, Mouse RPL39L integrated into the yeast 60S ribosomal subunit
8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8P8U 2.23 Å, Yeast 60S ribosomal subunit
8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

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