3J80: 40S-eIF1-eIF1A preinitiation complex
CryoEM structure of 40S-eIF1-eIF1A preinitiation complex. Determined by electron microscopy at 3.75 Å resolution. Released 5 Nov 2014.
- Method
- Electron microscopy
- Resolution
- 3.75 Å
- Organisms
- Kluyveromyces lactis, Saccharomyces cerevisiae
- Chains
- 37
- Atoms
- 77,716
- Mol. weight
- 1208.13 kDa
- Ligands
- ZN, MG
- Released
- 5 Nov 2014
Explore 3J80 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3J80 contains 184 α-helices and 258 β-strands across 36 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, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19 | 1 | |
| β-strand | 20-22 | 3 | 65 |
| α-helix | 23 | 1 | |
| β-strand | 29-31 | 3 | 65 |
| β-strand | 37-43 | 7 | 66 |
| α-helix | 47-56 | 10 | |
| β-strand | 66-72 | 7 | 66 |
| α-helix | 77-79 | 3 | |
Chain A: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| β-strand | 27 | 1 | 4 |
| β-strand | 37-41 | 5 | 4 |
| β-strand | 45-48 | 4 | 4 |
| α-helix | 50-64 | 15 | |
| β-strand | 73-77 | 5 | 5 |
| α-helix | 80-82 | 3 | |
| α-helix | 83-92 | 10 | |
| β-strand | 96-99 | 4 | 5 |
| β-strand | 120-123 | 4 | 5 |
| α-helix | 130-139 | 10 | |
| β-strand | 143-148 | 6 | 5 |
| β-strand | 159-162 | 4 | 5 |
| α-helix | 168-183 | 16 | |
| α-helix | 199-201 | 3 | |
Chain b: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 32-36 | 5 | 67 |
| β-strand | 43-47 | 5 | 67 |
| β-strand | 64-65 | 2 | 68 |
| β-strand | 72-73 | 2 | 68 |
| β-strand | 79 | 1 | 67 |
Chain B: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-33 | 7 | 9 |
| β-strand | 44-49 | 6 | 9 |
| α-helix | 57-61 | 5 | |
| β-strand | 65-68 | 4 | 9 |
| α-helix | 70-74 | 5 | |
| α-helix | 77-79 | 3 | |
| β-strand | 83-92 | 10 | 9 |
| β-strand | 95-104 | 10 | 9 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-128 | 9 | 9 |
| β-strand | 134-142 | 9 | 9 |
| α-helix | 143-144 | 2 | |
| α-helix | 158-175 | 18 | |
| α-helix | 182-188 | 7 | |
| α-helix | 192-201 | 10 | |
| β-strand | 208 | 1 | 9 |
| β-strand | 215-217 | 3 | 9 |
| α-helix | 225-229 | 5 | |
Chain c: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-11 | 2 | 26 |
| β-strand | 12-19 | 8 | 27 |
| β-strand | 25-31 | 7 | 27 |
| β-strand | 39-44 | 6 | 27 |
| β-strand | 53-54 | 2 | 26 |
Chain C: 9 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-52 | 8 | |
| α-helix | 58-63 | 6 | |
| α-helix | 72-77 | 6 | |
| β-strand | 82-94 | 13 | 12 |
| β-strand | 99-110 | 12 | 12 |
| β-strand | 115-116 | 2 | 13 |
| β-strand | 117-123 | 7 | 12 |
| α-helix | 126-140 | 15 | |
| β-strand | 142-143 | 2 | 13 |
| β-strand | 146-147 | 2 | 14 |
| β-strand | 158-159 | 2 | 14 |
| β-strand | 163-164 | 2 | 15 |
| β-strand | 167 | 1 | 15 |
| β-strand | 170-176 | 7 | 15 |
| β-strand | 183-184 | 2 | 15 |
| α-helix | 187-196 | 10 | |
| β-strand | 201-207 | 7 | 15 |
| α-helix | 212-226 | 15 | |
| α-helix | 232-234 | 3 | |
| α-helix | 241-243 | 3 | |
| α-helix | 244-246 | 3 | |
Chain d: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-18 | 4 | |
| β-strand | 30-31 | 2 | 32 |
| α-helix | 33-35 | 3 | |
| β-strand | 38-39 | 2 | 32 |
| α-helix | 40-46 | 7 | |
| β-strand | 53 | 1 | 11 |
Chain D: 6 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| β-strand | 34-41 | 8 | 69 |
| β-strand | 46-52 | 7 | 69 |
| α-helix | 55-59 | 5 | |
| α-helix | 65-77 | 13 | |
| β-strand | 81 | 1 | 69 |
| β-strand | 84-90 | 7 | 69 |
| α-helix | 98-111 | 14 | |
| α-helix | 115-129 | 15 | |
| β-strand | 133-139 | 7 | 70 |
| β-strand | 140 | 1 | 71 |
| β-strand | 148 | 1 | 71 |
| β-strand | 151-155 | 5 | 70 |
| β-strand | 168-175 | 8 | 70 |
| β-strand | 182-189 | 8 | 70 |
| β-strand | 206-208 | 3 | 72 |
| α-helix | 209-211 | 3 | |
| β-strand | 223-224 | 2 | 47 |
28 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 rRNA | 2 | RNA | 1799 | Kluyveromyces lactis | |
| uS2 | A | protein | 254 | Kluyveromyces lactis | Q6CN12 (AlphaFold model) |
| eS1 | B | protein | 255 | Kluyveromyces lactis | Q6CWD0 (AlphaFold model) |
| uS5 | C | protein | 259 | Kluyveromyces lactis | Q6CKL3 (AlphaFold model) |
| eS4 | E | protein | 261 | Kluyveromyces lactis | Q6CWJ2 (AlphaFold model) |
| eS6 | G | protein | 236 | Kluyveromyces lactis | Q6CM04 |
| eS7 | H | protein | 190 | Kluyveromyces lactis | Q6CTD6 |
| eS8 | I | protein | 201 | Kluyveromyces lactis | Q6CMG3 |
| uS4 | J | protein | 188 | Kluyveromyces lactis | Q6CM18 |
| uS17 | L | protein | 156 | Kluyveromyces lactis | Q6CX80 |
| uS15 | N | protein | 151 | Kluyveromyces lactis | Q6CJK0 |
| uS11 | O | protein | 137 | Kluyveromyces lactis | P27069 |
25 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>3J80_1 18S rRNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAA
AUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCU
UGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAA
UUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAAC
GGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAA
GGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGA
UACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGA
ACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUA
UUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGA
CUUUAUGUCGCGCACUGGUUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUU
GUGGGUGCAGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGA
AAGCUCGAAUAUAUUAGCAUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUU
AGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCC
UUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCC
GAGAGGUCUGGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUU
GCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCU
GCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGA
UUUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAU
UUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 2 (A), FASTA
>3J80_2 uS2 (chains A)
MSLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLA
ARIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALPDRTQPWAIMPDLYFYRNPEEIEQQTAEEEAVASGEQTEEAVDATEEQTEAA
EWAEEGQAQEEEWN
Sequence of entity 3 (B), FASTA
>3J80_3 eS1 (chains B)
MAVGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDS
LKGRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNST
LAQLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHGEASAEEK
GKKVAGFKDEILETV
Sequence of entity 4 (C), FASTA
>3J80_4 uS5 (chains C)
MSAPQAQGQQAPRRGGFGGANRGGRGGRRGGRRDQEEKGWVPVTKLGRLVKAGKISSIEE
IFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGI
KTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTSGKCGSVSVRLIPAPRG
SGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKAAFVAIGNTYGFLTPNLWEVQAL
TPSPMDVYADYATASKKKL
Sequence of entity 5 (E), FASTA
>3J80_5 eS4 (chains E)
MARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEAS
YKLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKL
VYVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPK
GKGIKLTISEERDRRRAQHGL
Sequence of entity 6 (G), FASTA
>3J80_6 eS6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEVRKRRASSLKA
Sequence of entity 7 (H), FASTA
>3J80_7 eS7 (chains H)
MSDPQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAV
FVPVPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQ
IVFEIPSETH
Sequence of entity 8 (I), FASTA
>3J80_8 eS8 (chains I)
MGISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRI
ETGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQS
LGKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRC
DGYILEGEELAFYLRRLTAKK
Sequence of entity 9 (J), FASTA
>3J80_9 uS4 (chains J)
MPRAPRTYSKTYSTPKRPYESARLDAELKLAGEYGLKNKREIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRIGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLISQRHIAVGKQIVNIPSFMVRLESEKHIDFARTSPFGGARPGRVARKRAAAA
GGEEADEE
Sequence of entity 10 (L), FASTA
>3J80_10 uS17 (chains L)
MSTELTVQSERAFQKQPHIFTNPKAKANRKTKRWYKNVGLGFKTPKTAIEGSYIDKKCPF
TGLVSIRGKILTGTVVSTRMHRTIVIRRDYLHYVPKYNRYEKRHKNVPAHVSPAFRVQVG
DIVTVGQCRPISKTVRFNVLKVASATGKANKQFAKF
Sequence of entity 11 (N), FASTA
>3J80_11 uS15 (chains N)
MGRMHSKGKGMSSSAIPYSRNAPAWFKGSSDGVVEQIIKYARKGLTPSQIGVLLRDAHGV
TQAKVITGNKILRILKSNGLAPEIPEDLYFLIKKAVSVRKHLERNRKDKDAKFRLILIES
RIHRLARYYRTVSVLPPNWKYESATASALVN
Sequence of entity 12 (O), FASTA
>3J80_12 uS11 (chains O)
MANVVQAKDNSQVFGVARIFASFNDTFVHVTDLSGRETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHIKIRATGGTRSKTPGPGGQAALRALARSGLRIGRIEDVTP
VPSDSTRKKGGRRGRRL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
| MG | Magnesium ion | Mg | 67 |
Primary citation
Structural changes enable start codon recognition by the eukaryotic translation initiation complex. Hussain, T., Llacer, J.L., Fernandez, I.S. et al. Cell (2014) 159:597-607. DOI 10.1016/j.cell.2014.10.001 · PubMed
Other PDB entries of the same protein (UniProt Q6CN12 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6FYY 3.02 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
- 8RW1 3.35 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation
- 8S8D 3.45 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
- 3JAM 3.46 Å, CryoEM structure of 40S-eIF1A-eIF1 complex from yeast
- 6FYX 3.5 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
- 5IT7 3.6 Å, Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis…
- 6UZ7 3.6 Å, K.lactis 80S ribosome with p/PE tRNA and eIF5B
- 5IT9 3.8 Å, Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the…
- 8S8E 3.85 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
- 8S8F 3.95 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
- 3J81 4.0 Å, CryoEM structure of a partial yeast 48S preinitiation complex
- 8S8G 4.0 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
Browse structure collections
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