6ZU9: Yeast ABCE1-bound 48S initiation complex
Structure of a yeast ABCE1-bound 48S initiation complex. Determined by electron microscopy at 6.2 Å resolution. Released 28 Oct 2020.
- Method
- Electron microscopy
- Resolution
- 6.2 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 44
- Atoms
- 78,384
- Mol. weight
- 1681.18 kDa
- Ligands
- MG, ZN, ADP, ATP
- Released
- 28 Oct 2020
Explore 6ZU9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6ZU9 contains 314 α-helices and 369 β-strands across 41 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: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 62 |
| β-strand | 8 | 1 | 62 |
| α-helix | 13-14 | 2 | |
| β-strand | 15-16 | 2 | 63 |
| β-strand | 23-24 | 2 | 63 |
| β-strand | 32-39 | 8 | 64 |
| β-strand | 45-55 | 11 | 64 |
| α-helix | 57-61 | 5 | |
| α-helix | 65-75 | 11 | |
Chain A: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-26 | 3 | |
| β-strand | 33-41 | 9 | 89 |
| β-strand | 47-51 | 5 | 89 |
| β-strand | 55-61 | 7 | 89 |
| β-strand | 76-81 | 6 | 89 |
| α-helix | 82 | 1 | |
| β-strand | 88-94 | 7 | 89 |
| α-helix | 97-106 | 10 | |
Chain b: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-20 | 15 | |
| β-strand | 24-27 | 4 | 32 |
| α-helix | 32-43 | 12 | |
| β-strand | 50-53 | 4 | 32 |
| β-strand | 60-64 | 5 | 32 |
| β-strand | 72-74 | 3 | 66 |
| β-strand | 80-81 | 2 | 66 |
| α-helix | 83-93 | 11 | |
| β-strand | 101-106 | 6 | 66 |
| β-strand | 109-112 | 4 | 66 |
| α-helix | 113-119 | 7 | |
| β-strand | 123-129 | 7 | 66 |
Chain B: 11 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| α-helix | 29-32 | 4 | |
| β-strand | 37-42 | 6 | 107 |
| β-strand | 45-52 | 8 | 107 |
| α-helix | 55-59 | 5 | |
| α-helix | 61-63 | 3 | |
| α-helix | 64-77 | 14 | |
| α-helix | 79-80 | 2 | |
| β-strand | 84-90 | 7 | 107 |
| α-helix | 94-96 | 3 | |
| α-helix | 98-111 | 14 | |
| α-helix | 115-128 | 14 | |
| β-strand | 131-141 | 11 | 108 |
| β-strand | 147-155 | 9 | 108 |
| α-helix | 162-167 | 6 | |
| β-strand | 168-177 | 10 | 108 |
| β-strand | 180-190 | 11 | 108 |
| β-strand | 207-208 | 2 | 109 |
| α-helix | 209-213 | 5 | |
| β-strand | 221-223 | 3 | 37 |
Chain c: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-24 | 13 | |
| α-helix | 28-34 | 7 | |
| α-helix | 36-39 | 4 | |
| β-strand | 48-57 | 10 | 83 |
| α-helix | 59 | 1 | |
| β-strand | 60 | 1 | 84 |
| α-helix | 61 | 1 | |
| β-strand | 68 | 1 | 84 |
| β-strand | 71-76 | 6 | 83 |
| β-strand | 82-86 | 5 | 83 |
| α-helix | 92-95 | 4 | |
| β-strand | 101-106 | 6 | 83 |
| β-strand | 122-127 | 6 | 83 |
| β-strand | 130-131 | 2 | 83 |
| α-helix | 132-136 | 5 | |
Chain C: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-38 | 8 | |
| α-helix | 82-85 | 4 | |
| α-helix | 89-97 | 9 | |
| α-helix | 101-103 | 3 | |
| α-helix | 107-123 | 17 | |
| α-helix | 129-139 | 11 | |
| β-strand | 144-149 | 6 | 45 |
| β-strand | 156-161 | 6 | 45 |
| α-helix | 164-183 | 20 | |
| α-helix | 190-203 | 14 | |
| α-helix | 209-223 | 15 | |
Chain d: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-15 | 8 | 86 |
| β-strand | 20-28 | 9 | 86 |
| α-helix | 37-48 | 12 | |
| α-helix | 52-54 | 3 | |
| β-strand | 55-62 | 8 | 86 |
| α-helix | 63 | 1 | |
| β-strand | 68-76 | 9 | 86 |
| α-helix | 79-85 | 7 | |
| α-helix | 88-93 | 6 | |
| α-helix | 105-115 | 11 | |
| α-helix | 123-132 | 10 | |
Chain D: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-18 | 14 | |
| β-strand | 20-22 | 3 | 110 |
| α-helix | 39-51 | 13 | |
| β-strand | 55-56 | 2 | 110 |
| β-strand | 65-68 | 4 | 110 |
| α-helix | 70-80 | 11 | |
33 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 | 1800 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
| 40S ribosomal protein S0-A | P | protein | 252 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32905 (AlphaFold model) |
| 40S ribosomal protein S1-A | Q | protein | 255 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33442 (AlphaFold model) |
| 40S ribosomal protein S2 | R | protein | 254 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25443 (AlphaFold model) |
| 40S ribosomal protein S4-A | S | protein | 261 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX35 (AlphaFold model) |
| 40S ribosomal protein S6-A | T | protein | 236 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX37 |
| 40S ribosomal protein S7-A | U | protein | 190 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26786 |
| 40S ribosomal protein S8-A | V | protein | 200 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX39 |
| 40S ribosomal protein S9-A | W | protein | 197 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | O13516 |
| 40S ribosomal protein S11-A | X | protein | 155 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX47 |
| 40S ribosomal protein S13 | Y | protein | 151 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P05756 |
| 40S ribosomal protein S14-A | Z | protein | 136 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P06367 |
32 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>6ZU9_1 18S ribosomal RNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCG
AUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUG
UGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUA
UUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCU
UAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCC
CUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGC
CGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAU
UGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCC
UGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGG
AUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCA
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 2 (P), FASTA
>6ZU9_2 40S ribosomal protein S0-A (chains P)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW
Sequence of entity 3 (Q), FASTA
>6ZU9_3 40S ribosomal protein S1-A (chains Q)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV
Sequence of entity 4 (R), FASTA
>6ZU9_4 40S ribosomal protein S2 (chains R)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF
Sequence of entity 5 (S), FASTA
>6ZU9_5 40S ribosomal protein S4-A (chains S)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL
Sequence of entity 6 (T), FASTA
>6ZU9_6 40S ribosomal protein S6-A (chains T)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA
Sequence of entity 7 (U), FASTA
>6ZU9_7 40S ribosomal protein S7-A (chains U)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH
Sequence of entity 8 (V), FASTA
>6ZU9_8 40S ribosomal protein S8-A (chains V)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK
Sequence of entity 9 (W), FASTA
>6ZU9_9 40S ribosomal protein S9-A (chains W)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE
Sequence of entity 10 (X), FASTA
>6ZU9_10 40S ribosomal protein S11-A (chains X)
STELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFT
GLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGD
IVTVGQCRPISKTVRFNVVKVSAAAAKANKQFAKF
Sequence of entity 11 (Y), FASTA
>6ZU9_11 40S ribosomal protein S13 (chains Y)
MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGV
TQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIES
RIHRLARYYRTVAVLPPNWKYESATASALVN
Sequence of entity 12 (Z), FASTA
>6ZU9_12 40S ribosomal protein S14-A (chains Z)
SNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAM
LAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPV
PSDSTRKKGGRRGRRL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 4 |
| ZN | Zinc ion | Zn | 3 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
Primary citation
A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. Kratzat, H., Mackens-Kiani, T., Ameismeier, M. et al. EMBO J (2021) 40:e105179-e105179. DOI 10.15252/embj.2020105179 · PubMed
Other PDB entries of the same protein (UniProt P32905 (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…
- 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,…
- 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
- 8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 7ZW0 2.4 Å, FAP-80S Complex - Rotated state
- 8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing
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