6ZCE: Yeast ABCE1-bound 43S pre-initiation complex
Structure of a yeast ABCE1-bound 43S pre-initiation complex. Determined by electron microscopy at 5.3 Å resolution. Released 7 Oct 2020.
- Method
- Electron microscopy
- Resolution
- 5.3 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae S288C
- Chains
- 45
- Atoms
- 76,380
- Mol. weight
- 1700.89 kDa
- Ligands
- SF4, ATP, MG, ADP
- Released
- 7 Oct 2020
Explore 6ZCE in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6ZCE contains 313 α-helices and 373 β-strands across 44 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, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-53 | 9 | |
| α-helix | 62-66 | 5 | |
| α-helix | 73-83 | 11 | |
| β-strand | 90-91 | 2 | 12 |
| β-strand | 101-102 | 2 | 12 |
Chain b: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 15 |
| β-strand | 29-31 | 3 | 15 |
| α-helix | 32-34 | 3 | |
| β-strand | 37-42 | 6 | 16 |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 94 |
| β-strand | 67-72 | 6 | 16 |
Chain B: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| β-strand | 24 | 1 | 13 |
| β-strand | 37-41 | 5 | 13 |
| β-strand | 45-48 | 4 | 13 |
| α-helix | 50-64 | 15 | |
| α-helix | 70-72 | 3 | |
| β-strand | 73-77 | 5 | 14 |
| α-helix | 80-92 | 13 | |
| β-strand | 96-99 | 4 | 14 |
| β-strand | 120-123 | 4 | 14 |
| α-helix | 130-138 | 9 | |
| β-strand | 143-147 | 5 | 14 |
| β-strand | 159-161 | 3 | 14 |
| α-helix | 169-182 | 14 | |
Chain c: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 32-37 | 6 | 19 |
| β-strand | 40-47 | 8 | 19 |
| β-strand | 64-65 | 2 | 20 |
| β-strand | 72-73 | 2 | 20 |
| β-strand | 78-80 | 3 | 19 |
Chain C: 11 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-25 | 3 | |
| β-strand | 29-31 | 3 | 17 |
| β-strand | 32 | 1 | 18 |
| β-strand | 33 | 1 | 17 |
| β-strand | 42-47 | 6 | 17 |
| α-helix | 57-60 | 4 | |
| β-strand | 65-69 | 5 | 18 |
| α-helix | 70-72 | 3 | |
| α-helix | 77-79 | 3 | |
| β-strand | 83-92 | 10 | 18 |
| β-strand | 95-103 | 9 | 18 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-128 | 9 | 18 |
| β-strand | 134-142 | 9 | 18 |
| α-helix | 145-146 | 2 | |
| α-helix | 159-175 | 17 | |
| α-helix | 182-188 | 7 | |
| α-helix | 192-202 | 11 | |
| β-strand | 208-211 | 4 | 18 |
| β-strand | 215-219 | 5 | 18 |
| α-helix | 225-228 | 4 | |
| α-helix | 229-231 | 3 | |
Chain d: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-19 | 12 | 24 |
| β-strand | 25-32 | 8 | 24 |
| β-strand | 39-44 | 6 | 24 |
| β-strand | 53-56 | 4 | 24 |
Chain D: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-47 | 9 | |
| α-helix | 53-58 | 6 | |
| α-helix | 66-72 | 7 | |
| β-strand | 77-89 | 13 | 21 |
| β-strand | 94-105 | 12 | 21 |
| β-strand | 110-117 | 8 | 21 |
| α-helix | 121-134 | 14 | |
| β-strand | 137-138 | 2 | 21 |
| β-strand | 141-142 | 2 | 22 |
| β-strand | 153-154 | 2 | 22 |
| β-strand | 158-162 | 5 | 23 |
| β-strand | 165-171 | 7 | 23 |
| β-strand | 178 | 1 | 23 |
| α-helix | 182-189 | 8 | |
| β-strand | 196-201 | 6 | 23 |
| α-helix | 207-218 | 12 | |
| α-helix | 221-223 | 3 | |
| α-helix | 227-229 | 3 | |
| α-helix | 239-242 | 4 | |
Chain e: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 30-31 | 2 | 28 |
| α-helix | 33-35 | 3 | |
| β-strand | 38-39 | 2 | 28 |
| α-helix | 40-46 | 7 | |
| β-strand | 53 | 1 | 115 |
36 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 |
|---|
| Eukaryotic translation initiation factor 3 subunit I | l | protein | 347 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40217 (AlphaFold model) |
| Eukaryotic translation initiation factor 3 subunit G | r | protein | 274 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q04067 (AlphaFold model) |
| 18S ribosomal RNA (1719-MER) | A | RNA | 1800 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
| 40S ribosomal protein S0-A | B | protein | 252 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32905 (AlphaFold model) |
| 40S ribosomal protein S1-A | C | protein | 255 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33442 (AlphaFold model) |
| 40S ribosomal protein S2 | D | protein | 254 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25443 |
| 40S ribosomal protein S3 | E | protein | 240 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P05750 |
| 40S ribosomal protein S4-A | F | protein | 261 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX35 |
| 40S ribosomal protein S5 | G | protein | 225 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26783 |
| 40S ribosomal protein S6-A | H | protein | 236 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX37 |
| 40S ribosomal protein S7-A | I | protein | 190 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26786 |
| 40S ribosomal protein S8-A | J | protein | 200 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX39 |
32 more molecules are not listed.
Sequence of entity 1 (l), FASTA
>6ZCE_1 Eukaryotic translation initiation factor 3 subunit I (chains l)
MKAIKLTGHERPLTQVKYNKEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDV
DCFTKYCVTGSADYSIKLWDVSNGQCVATWKSPVPVKRVEFSPCGNYFLAILDNVMKNPG
SINIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIAGHKDGKISKY
DVSNNYEYVDSIDLHEKSISDMQFSPDLTYFITSSRDTNSFLVDVSTLQVLKKYETDCPL
NTAVITPLKEFIILGGGQEAKDVTTTSANEGKFEARFYHKIFEEEIGRVQGHFGPLNTVA
ISPQGTSYASGGEDGFIRLHHFEKSYFDFKYDVEKAAEAKEHMQEAN
Sequence of entity 2 (r), FASTA
>6ZCE_2 Eukaryotic translation initiation factor 3 subunit G (chains r)
MSEVAPEEIIENADGSRSIITYKIEDGVKYKITQKVKEVKVLEKVHKSVAERKNWHKYGS
EKGSPAGPSAVTARLGEEVELRLSRNWKQAEEERIQKEKASLTKTGLQCRLCGNDHMTMN
CPFKTILSELSALEDPATSEGGVEAASEEKAGQVGGAGSIPGQYVPPSRRAGARDPSSDA
YRDSRERDDMCTLKIMQVNENADENSLREELLFPFAPIPRVSVVRNKETGKSRGLAFVTF
SSEEVAEQALRFLDGRGYMNLILRVEWSKPKVKE
Sequence of entity 3 (A), FASTA
>6ZCE_3 18S ribosomal RNA (1719-MER) (chains A)
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 4 (B), FASTA
>6ZCE_4 40S ribosomal protein S0-A (chains B)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW
Sequence of entity 5 (C), FASTA
>6ZCE_5 40S ribosomal protein S1-A (chains C)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV
Sequence of entity 6 (D), FASTA
>6ZCE_6 40S ribosomal protein S2 (chains D)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF
Sequence of entity 7 (E), FASTA
>6ZCE_7 40S ribosomal protein S3 (chains E)
MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG
ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQG
VLGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA
Sequence of entity 8 (F), FASTA
>6ZCE_8 40S ribosomal protein S4-A (chains F)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL
Sequence of entity 9 (G), FASTA
>6ZCE_9 40S ribosomal protein S5 (chains G)
MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD
YVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDI
INVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAR
EAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 10 (H), FASTA
>6ZCE_10 40S ribosomal protein S6-A (chains H)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA
Sequence of entity 11 (I), FASTA
>6ZCE_11 40S ribosomal protein S7-A (chains I)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH
Sequence of entity 12 (J), FASTA
>6ZCE_12 40S ribosomal protein S8-A (chains J)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| MG | Magnesium ion | Mg | 2 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| ZN | Zinc ion | Zn | 4 |
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 P40217 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3ZWL 2.2 Å, Structure of eukaryotic translation initiation factor eIF3i complex with eIF3b…
- 8CAH 3.0 Å, Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex
- 8CAS 3.3 Å, Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)
- 6FYX 3.5 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
- 3JAP 4.9 Å, Structure of a partial yeast 48S preinitiation complex in closed conformation
- 6GSM 5.15 Å, Structure of a partial yeast 48S preinitiation complex in open conformation.
- 6GSN 5.75 Å, Structure of a partial yeast 48S preinitiation complex in closed conformation
- 9CPA 6.0 Å, Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex
- 6ZU9 6.2 Å, Structure of a yeast ABCE1-bound 48S initiation complex
- 5A5U 9.0 Å, Structure of mammalian eIF3 in the context of the 43S preinitiation complex
Browse structure collections
About this viewer
MolViewer shows 6ZCE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.