6Q8Y: 60S ribosomal protein L8-A

Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex. Determined by electron microscopy at 3.1 Å resolution. Released 13 Mar 2019.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Saccharomyces cerevisiae
Chains: 82
Atoms: 209,410
Mol. weight: 3180.01 kDa
Ligands: ZN, MG
Released: 13 Mar 2019

Explore 6Q8Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q8Y contains 522 α-helices and 546 β-strands across 75 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	166
β-strand	6-8	3	166
α-helix	13-14	2
β-strand	15-17	3	167
β-strand	22-24	3	167
β-strand	32-37	6	168
α-helix	38-39	2
β-strand	40	1	169
β-strand	43	1	169
β-strand	50-55	6	168
α-helix	57-62	6
α-helix	65-76	12

Chain A: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-42	9	29
β-strand	45-52	8	29
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-86	3	29
β-strand	89-90	2	29
α-helix	91	1
α-helix	92-94	3
α-helix	98-111	14
α-helix	115-129	15
β-strand	133-140	8	30
β-strand	148-154	7	30
α-helix	162-166	5
β-strand	169-177	9	30
β-strand	180-189	10	30
β-strand	208	1	31
α-helix	209-211	3
α-helix	213-215	3
β-strand	221-224	4	32

Chain AA: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	51	1	5
α-helix	54-68	15
α-helix	84-96	13
α-helix	102-118	17
α-helix	127-129	3
α-helix	131-132	2
β-strand	133	1	6
α-helix	136-144	9
β-strand	150-154	5	6
α-helix	160-162	3
α-helix	165-173	9
β-strand	177-180	4	6
α-helix	183-190	8
β-strand	197-200	4	6
α-helix	208-218	11
α-helix	219-223	5
α-helix	226-231	6
α-helix	240-249	10
α-helix	251-253	3

Chain AB: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	9
β-strand	21-25	5	10
β-strand	27	1	11
β-strand	33-39	7	10
α-helix	48-50	3
β-strand	51-52	2	9
β-strand	57-61	5	10
β-strand	74-80	7	10
β-strand	85-86	2	12
β-strand	92-95	4	12
β-strand	99-102	4	10
β-strand	103	1	13
β-strand	109	1	13
β-strand	114	1	11
β-strand	118	1	14
α-helix	120-125	6
α-helix	127-132	6
β-strand	133	1	11
β-strand	136	1	14

Chain AC: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	19	1	17
α-helix	22-25	4
α-helix	36-48	13
α-helix	52-76	25
α-helix	80-97	18

Chain AD: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-11	9	23
β-strand	17-21	5	24
β-strand	24-28	5	24
β-strand	33-36	4	24
β-strand	44-47	4	23
β-strand	52-60	9	23
α-helix	62-83	22
β-strand	86-93	8	25
α-helix	98-99	2
β-strand	100-104	5	26
β-strand	111-115	5	26
α-helix	117-119	3
β-strand	124-127	4	26
α-helix	128-129	2
β-strand	132-136	5	25
β-strand	143-148	6	25
α-helix	151-164	14
β-strand	178-186	9	25

Chain AE: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	33
β-strand	12-13	2	33
β-strand	19-22	4	12
β-strand	28-31	4	12
α-helix	34-41	8
α-helix	53-58	6

Chain AF: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
β-strand	16-17	2	37
β-strand	27-28	2	37
β-strand	34	1	37
α-helix	44-45	2
α-helix	51-57	7
α-helix	67-76	10

67 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
18S ribosomal RNA	2	RNA	1797	Saccharomyces cerevisiae
60S ribosomal protein L8-A	AA	protein	233	Saccharomyces cerevisiae	P17076 (AlphaFold model)
60S ribosomal protein L23-A	AB	protein	136	Saccharomyces cerevisiae	P0CX41 (AlphaFold model)
60S ribosomal protein L36-A	AC	protein	100	Saccharomyces cerevisiae	P05745 (AlphaFold model)
60S ribosomal protein L9-A	AD	protein	191	Saccharomyces cerevisiae	P05738 (AlphaFold model)
60S ribosomal protein L24-A	AE	protein	67	Saccharomyces cerevisiae	P04449
60S ribosomal protein L37-A	AF	protein	87	Saccharomyces cerevisiae	P49166
60S ribosomal protein L11-B	AG	protein	169	Saccharomyces cerevisiae	Q3E757
60S ribosomal protein L25	AH	protein	121	Saccharomyces cerevisiae	P04456
60S ribosomal protein L38	AI	protein	77	Saccharomyces cerevisiae	P49167
60S ribosomal protein L13-A	AJ	protein	193	Saccharomyces cerevisiae	Q12690
60S ribosomal protein L26-A	AK	protein	126	Saccharomyces cerevisiae	P05743

70 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>6Q8Y_1 18S ribosomal RNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCG
AUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGU
GGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAU
UGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUU
CUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAG
GUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUU
CAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAAC
CAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUA
CGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGG
AAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGG
AAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUG
UGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUA
ACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUU
AGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCC
UUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCC
GAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUU
GCUCUUCAGCGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCU
GCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGA
UCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAU
UUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAU

Sequence of entity 2 (AA), FASTA

>6Q8Y_2 60S ribosomal protein L8-A (chains AA)
NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYTLD
RNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALI
ENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEV
RAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA

Sequence of entity 3 (AB), FASTA

>6Q8Y_3 60S ribosomal protein L23-A (chains AB)
SGNGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMAT
VKKGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGKE
CADLWPRVASNSGVVV

Sequence of entity 4 (AC), FASTA

>6Q8Y_4 60S ribosomal protein L36-A (chains AC)
MTVKTGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDL
IRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASRRH

Sequence of entity 5 (AD), FASTA

>6Q8Y_5 60S ribosomal protein L9-A (chains AD)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 6 (AE), FASTA

>6Q8Y_6 60S ribosomal protein L24-A (chains AE)
MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIAWTVLFRKHHK
KGITEEV

Sequence of entity 7 (AF), FASTA

>6Q8Y_7 60S ribosomal protein L37-A (chains AF)
GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGT
GRMRYLKHVSRRFKNGFQTGSASKASA

Sequence of entity 8 (AG), FASTA

>6Q8Y_8 60S ribosomal protein L11-B (chains AG)
QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVRTFGIRRNEKI
AVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFGIDEHIDLGIKYDPSIGIFGM
DFYVVMNRPGARVTRRKRCKGTVGNSHKTTKEDTVSWFKQKYDADVLDK

Sequence of entity 9 (AH), FASTA

>6Q8Y_9 60S ribosomal protein L25 (chains AH)
KALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSETAMKKVEDGNI
LVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKKAYVRLTADYDALDIANRIGY
I

Sequence of entity 10 (AI), FASTA

>6Q8Y_10 60S ribosomal protein L38 (chains AI)
AREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSLYTLVINDAGK
AKKLIQSLPPTLKVNRL

Sequence of entity 11 (AJ), FASTA

>6Q8Y_11 60S ribosomal protein L13-A (chains AJ)
AISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRAP
TVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQS
KIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFRG
IREKRAREKAEAE

Sequence of entity 12 (AK), FASTA

>6Q8Y_12 60S ribosomal protein L26-A (chains AK)
AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVRG
SKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQR
KGGKLE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
MG	Magnesium ion	Mg	2

Primary citation

Structure of the 80S ribosome-Xrn1 nuclease complex. Tesina, P., Heckel, E., Cheng, J. et al. Nat Struct Mol Biol (2019) 26:275-280. DOI 10.1038/s41594-019-0202-5 · PubMed

Other PDB entries of the same protein (UniProt P17076 (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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