10ZY: 60S ribosomal protein L8-A
Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP. Determined by electron microscopy at 2.74 Å resolution. Released 1 Jul 2026.
- Method
- Electron microscopy
- Resolution
- 2.74 Å
- Organism
- Saccharomyces cerevisiae S288C
- Chains
- 7
- Atoms
- 11,940
- Mol. weight
- 1308.68 kDa
- Ligands
- MG
- Released
- 1 Jul 2026
Explore 10ZY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
10ZY contains 51 α-helices and 59 β-strands across 6 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 b: 9 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-8 | 6 | |
| β-strand | 33-37 | 5 | 12 |
| α-helix | 43-55 | 13 | |
| β-strand | 59-61 | 3 | 12 |
| α-helix | 63-65 | 3 | |
| α-helix | 73-80 | 8 | |
| β-strand | 85-92 | 8 | 12 |
| β-strand | 96-102 | 7 | 12 |
| β-strand | 109-118 | 10 | 12 |
| β-strand | 130 | 1 | 13 |
| β-strand | 133 | 1 | 14 |
| α-helix | 134-135 | 2 | |
| β-strand | 136-139 | 4 | 12 |
| α-helix | 141-144 | 4 | |
| α-helix | 147-160 | 14 | |
| α-helix | 162-163 | 2 | |
| β-strand | 170 | 1 | 14 |
| β-strand | 175-182 | 8 | 12 |
| β-strand | 185-195 | 11 | 12 |
| β-strand | 210-229 | 20 | 12 |
| β-strand | 232-238 | 7 | 12 |
| α-helix | 245-270 | 26 | |
Chain G: 15 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 67-70 | 4 | 1 |
| α-helix | 71-72 | 2 | |
| α-helix | 73-76 | 4 | |
| α-helix | 77-79 | 3 | |
| α-helix | 81-83 | 3 | |
| α-helix | 84-95 | 12 | |
| α-helix | 98-100 | 3 | |
| α-helix | 102-117 | 16 | |
| α-helix | 122-125 | 4 | |
| α-helix | 127-129 | 3 | |
| β-strand | 133-134 | 2 | 2 |
| α-helix | 136-144 | 9 | |
| β-strand | 150-154 | 5 | 2 |
| α-helix | 160-162 | 3 | |
| α-helix | 166-173 | 8 | |
| β-strand | 177-180 | 4 | 2 |
| α-helix | 183-189 | 7 | |
| β-strand | 197-200 | 4 | 2 |
| α-helix | 205-207 | 3 | |
| α-helix | 208-219 | 12 | |
Chain i: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-48 | 12 | |
| α-helix | 52-64 | 13 | |
| α-helix | 66-77 | 12 | |
| α-helix | 80-96 | 17 | |
Chain m: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 198-208 | 11 | |
| α-helix | 212-214 | 3 | |
| α-helix | 217-219 | 3 | |
| β-strand | 222-224 | 3 | 12 |
| α-helix | 230-232 | 3 | |
| α-helix | 239-263 | 25 | |
| α-helix | 270-271 | 2 | |
| β-strand | 274-276 | 3 | 9 |
| β-strand | 278 | 1 | 13 |
| α-helix | 282-291 | 10 | |
Chain N: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-10 | 7 | |
| α-helix | 17-31 | 15 | |
| β-strand | 36-39 | 4 | 3 |
| α-helix | 45-50 | 6 | |
| β-strand | 59-67 | 9 | 3 |
| α-helix | 98-109 | 12 | |
| β-strand | 114-123 | 10 | 3 |
| β-strand | 127-135 | 9 | 3 |
| α-helix | 140-143 | 4 | |
| α-helix | 149-152 | 4 | |
| α-helix | 154-156 | 3 | |
Chain R: 9 helices, 34 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 4 |
| β-strand | 7-8 | 2 | 4 |
| α-helix | 64-66 | 3 | |
| α-helix | 69-73 | 5 | |
| α-helix | 77-79 | 3 | |
| β-strand | 82-83 | 2 | 1 |
| β-strand | 96-97 | 2 | 1 |
| α-helix | 102-105 | 4 | |
| β-strand | 111-113 | 3 | 1 |
| β-strand | 122-125 | 4 | 1 |
| β-strand | 145-153 | 9 | 4 |
| β-strand | 156-165 | 10 | 4 |
| β-strand | 168 | 1 | 5 |
| β-strand | 193 | 1 | 5 |
| β-strand | 196-204 | 9 | 4 |
| β-strand | 209-217 | 9 | 6 |
| β-strand | 226-234 | 9 | 6 |
| β-strand | 239-243 | 5 | 6 |
| β-strand | 254-256 | 3 | 6 |
| β-strand | 289-294 | 6 | 7 |
| β-strand | 301-306 | 6 | 7 |
| β-strand | 311-315 | 5 | 7 |
| β-strand | 320-325 | 6 | 7 |
| β-strand | 334-339 | 6 | 8 |
| β-strand | 346-351 | 6 | 8 |
| β-strand | 355-360 | 6 | 8 |
| β-strand | 370-374 | 5 | 8 |
| β-strand | 381-386 | 6 | 9 |
| β-strand | 391-396 | 6 | 9 |
| β-strand | 400-405 | 6 | 9 |
| β-strand | 416-419 | 4 | 9 |
| β-strand | 425-430 | 6 | 10 |
| β-strand | 437-442 | 6 | 10 |
| β-strand | 447-452 | 6 | 10 |
| β-strand | 465-471 | 7 | 10 |
| β-strand | 477-482 | 6 | 11 |
| α-helix | 486-488 | 3 | |
| β-strand | 491-496 | 6 | 11 |
| α-helix | 500 | 1 | |
| β-strand | 501-505 | 5 | 11 |
| α-helix | 506-508 | 3 | |
| α-helix | 510-515 | 6 | |
| α-helix | 517-534 | 18 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 25S ribosomal RNA | 1 | RNA | 3396 | Saccharomyces cerevisiae S288C | |
| 60S ribosomal protein L8-A | G | protein | 256 | Saccharomyces cerevisiae S288C | P17076 (AlphaFold model) |
| 60S ribosomal protein L15-A | N | protein | 204 | Saccharomyces cerevisiae S288C | P05748 (AlphaFold model) |
| Periodic tryptophan protein 1 | R | protein | 576 | Saccharomyces cerevisiae S288C | P21304 (AlphaFold model) |
| Ribosome biogenesis protein BRX1 | b | protein | 291 | Saccharomyces cerevisiae S288C | Q08235 (AlphaFold model) |
| 60S ribosomal protein L36-A | i | protein | 100 | Saccharomyces cerevisiae S288C | P05745 |
| rRNA-processing protein EBP2 | m | protein | 427 | Saccharomyces cerevisiae S288C | P36049 |
Sequence of entity 1 (1), FASTA
>10ZY_1 25S ribosomal RNA (chains 1)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU
Sequence of entity 2 (G), FASTA
>10ZY_2 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA
Sequence of entity 3 (N), FASTA
>10ZY_3 60S ribosomal protein L15-A (chains N)
MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFV
IYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYW
VNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKF
NNTKAGRRKTWKRQNTLSLWRYRK
Sequence of entity 4 (R), FASTA
>10ZY_4 Periodic tryptophan protein 1 (chains R)
MISATNWVPRGFSSEFPEKYVLDDEEVERINQLAQLNLDDAKATLEEAEGESGVEDDAAT
GSSNKLKDQLDIDDDLKEYNLEEYDDEEIADNEGGKDVSMFPGLSNDSDVKFHEGEKGED
PYISLPNQEDSQEEKQELQVYPSDNLVLAARTEDDVSYLDIYVYDDGAGFHSSDIPVEEG
DEADPDVARGLVRDPALYVHHDLMLPAFPLCVEWLDYKVGSNSEEAANYAAIGTFDPQIE
IWNLDCVDKAFPDMILGEPLDNSMVSLKSKKKKKKSKTGHITTHHTDAVLSMAHNKYFRS
VLASTSADHTVKLWDLNSGNAARSLASIHSNKNVSSSEWHMLNGSILLTGGYDSRVALTD
VRISDESQMSKYWSAMAGEEIETVTFASENIILCGTDSGNVYSFDIRNNENRKPVWTLKA
HDAGISTLCSNKFIPGMMSTGAMGEKTVKLWKFPLDDATNTKGPSMVLSRDFDVGNVLTS
SFAPDIEVAGTMVIGGVNKVLKLWDVFTNRSVRKSFKSELENVQARAKEEAQKIGKSSRI
ARKYTSNDNPDTVITIDDQGEDEEEREGGDEHDDMA
Sequence of entity 5 (b), FASTA
>10ZY_5 Ribosome biogenesis protein BRX1 (chains b)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
Sequence of entity 6 (i), FASTA
>10ZY_6 60S ribosomal protein L36-A (chains i)
MTVKTGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDL
IRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASRRH
Sequence of entity 7 (m), FASTA
>10ZY_7 rRNA-processing protein EBP2 (chains m)
MAKGFKLKELLSHQKEIEKAEKLENDLKKKKSQELKKEEPTIVTASNLKKLEKKEKKADV
KKEVAADTEEYQSQALSKKEKRKLKKELKKMQEQDATEAQKHMSGDEDESGDDREEEEEE
EEEEEGRLDLEKLAKSDSESEDDSESENDSEEDEDVVAKEESEEKEEQEEEQDVPLSDVE
FDSDADVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDT
ERELAFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKK
AREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSLKNKRKHNEIDHSEFNVGVEE
EVEGKRFDRGRPNGKRAAKNAKYGQGGMKRFKRKNDATSSADVSGFSSRKMKGKTNRPGK
SRRARRF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 3 |
Primary citation
Mechanism for the initiation of co-transcriptional pre-60 S assembly. Piwowarczyk, R., Klinge, S. bioRxiv (2026). DOI 10.64898/2026.05.22.727207 · 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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