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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