3J81: Partial yeast 48S preinitiation complex
CryoEM structure of a partial yeast 48S preinitiation complex. Determined by electron microscopy at 4.0 Å resolution. Released 5 Nov 2014.
- Method
- Electron microscopy
- Resolution
- 4.0 Å
- Organisms
- Kluyveromyces lactis, Saccharomyces cerevisiae, synthetic construct
- Chains
- 42
- Atoms
- 83,760
- Mol. weight
- 1364.52 kDa
- Ligands
- MET, ZN, MG
- Released
- 5 Nov 2014
Explore 3J81 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3J81 contains 194 α-helices and 287 β-strands across 39 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: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 4 |
| β-strand | 29-31 | 3 | 4 |
| β-strand | 40-43 | 4 | 5 |
| α-helix | 51-55 | 5 | |
| β-strand | 66-69 | 4 | 5 |
| α-helix | 75-78 | 4 | |
Chain A: 7 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| β-strand | 24-25 | 2 | 2 |
| β-strand | 37-40 | 4 | 2 |
| β-strand | 46-48 | 3 | 2 |
| α-helix | 50-64 | 15 | |
| β-strand | 74-77 | 4 | 3 |
| α-helix | 83-91 | 9 | |
| β-strand | 97-99 | 3 | 3 |
| β-strand | 121-123 | 3 | 3 |
| α-helix | 130-138 | 9 | |
| β-strand | 143-145 | 3 | 3 |
| α-helix | 170-183 | 14 | |
| α-helix | 194-195 | 2 | |
| α-helix | 199-202 | 4 | |
Chain b: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 33-36 | 4 | 8 |
| β-strand | 44-46 | 3 | 8 |
| β-strand | 55 | 1 | 9 |
| β-strand | 62 | 1 | 9 |
| β-strand | 64-66 | 3 | 10 |
| β-strand | 71-73 | 3 | 10 |
| β-strand | 78-80 | 3 | 8 |
Chain B: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 29-33 | 5 | 6 |
| β-strand | 42-47 | 6 | 6 |
| β-strand | 65-69 | 5 | 6 |
| α-helix | 70-73 | 4 | |
| α-helix | 77-79 | 3 | |
| β-strand | 83-92 | 10 | 6 |
| β-strand | 95-104 | 10 | 6 |
| α-helix | 107-113 | 7 | |
| α-helix | 119 | 1 | |
| β-strand | 120-128 | 9 | 7 |
| β-strand | 134-142 | 9 | 7 |
| α-helix | 159-175 | 17 | |
| α-helix | 182-188 | 7 | |
| α-helix | 193-201 | 9 | |
| β-strand | 208-211 | 4 | 7 |
| β-strand | 215-219 | 5 | 7 |
| α-helix | 226-230 | 5 | |
Chain c: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-18 | 11 | 14 |
| α-helix | 25 | 1 | |
| β-strand | 26-32 | 7 | 14 |
| β-strand | 39-45 | 7 | 14 |
| β-strand | 53-56 | 4 | 14 |
Chain C: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-52 | 8 | |
| α-helix | 58-64 | 7 | |
| α-helix | 72-77 | 6 | |
| β-strand | 84-91 | 8 | 11 |
| β-strand | 102-110 | 9 | 11 |
| β-strand | 115-123 | 9 | 11 |
| α-helix | 126-140 | 15 | |
| β-strand | 142-143 | 2 | 11 |
| β-strand | 146-147 | 2 | 12 |
| β-strand | 158-159 | 2 | 12 |
| β-strand | 163-166 | 4 | 13 |
| β-strand | 171-176 | 6 | 13 |
| β-strand | 184 | 1 | 13 |
| α-helix | 187-196 | 10 | |
| β-strand | 201-206 | 6 | 13 |
| α-helix | 212-227 | 16 | |
| α-helix | 239-243 | 5 | |
| α-helix | 244-247 | 4 | |
| α-helix | 249-252 | 4 | |
Chain d: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-31 | 2 | 38 |
| α-helix | 33-35 | 3 | |
| β-strand | 38-39 | 2 | 38 |
| α-helix | 40-44 | 5 | |
| α-helix | 47-50 | 4 | |
| β-strand | 53 | 1 | 83 |
Chain D: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| β-strand | 34-41 | 8 | 15 |
| β-strand | 46-52 | 7 | 15 |
| α-helix | 55-59 | 5 | |
| α-helix | 64-76 | 13 | |
| β-strand | 84-90 | 7 | 15 |
| α-helix | 98-111 | 14 | |
| α-helix | 115-129 | 15 | |
| β-strand | 134-140 | 7 | 16 |
| β-strand | 148-154 | 7 | 16 |
| β-strand | 168-176 | 9 | 16 |
| β-strand | 181-189 | 9 | 16 |
| α-helix | 192-195 | 4 | |
| β-strand | 207 | 1 | 17 |
| α-helix | 208-213 | 6 | |
31 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) |
| uS3 | D | protein | 237 | Kluyveromyces lactis | Q6CRK7 (AlphaFold model) |
| eS4 | E | protein | 261 | Kluyveromyces lactis | Q6CWJ2 |
| uS7 | F | protein | 227 | Kluyveromyces lactis | Q6CRA3 |
| 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 |
| eS10 | K | protein | 106 | Kluyveromyces lactis | Q6CVZ5 |
30 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>3J81_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
>3J81_2 uS2 (chains A)
MSLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLA
ARIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALPDRTQPWAIMPDLYFYRNPEEIEQQTAEEEAVASGEQTEEAVDATEEQTEAA
EWAEEGQAQEEEWN
Sequence of entity 3 (B), FASTA
>3J81_3 eS1 (chains B)
MAVGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDS
LKGRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNST
LAQLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHGEASAEEK
GKKVAGFKDEILETV
Sequence of entity 4 (C), FASTA
>3J81_4 uS5 (chains C)
MSAPQAQGQQAPRRGGFGGANRGGRGGRRGGRRDQEEKGWVPVTKLGRLVKAGKISSIEE
IFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGI
KTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTSGKCGSVSVRLIPAPRG
SGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKAAFVAIGNTYGFLTPNLWEVQAL
TPSPMDVYADYATASKKKL
Sequence of entity 5 (D), FASTA
>3J81_5 uS3 (chains D)
MVAIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVG
ENGRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQG
VLGIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDYRPTEPVEAAESA
Sequence of entity 6 (E), FASTA
>3J81_6 eS4 (chains E)
MARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEAS
YKLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKL
VYVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPK
GKGIKLTISEERDRRRAQHGL
Sequence of entity 7 (F), FASTA
>3J81_7 uS7 (chains F)
MSEHEAQVEVEVQEDFEVVQEFVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASL
VDYIQISKPIYVAHTAGRYANKRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTL
EIINVLTDQNPLQVVVDAIINSGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIG
AREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 8 (G), FASTA
>3J81_8 eS6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEVRKRRASSLKA
Sequence of entity 9 (H), FASTA
>3J81_9 eS7 (chains H)
MSDPQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAV
FVPVPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQ
IVFEIPSETH
Sequence of entity 10 (I), FASTA
>3J81_10 eS8 (chains I)
MGISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRI
ETGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQS
LGKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRC
DGYILEGEELAFYLRRLTAKK
Sequence of entity 11 (J), FASTA
>3J81_11 uS4 (chains J)
MPRAPRTYSKTYSTPKRPYESARLDAELKLAGEYGLKNKREIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRIGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLISQRHIAVGKQIVNIPSFMVRLESEKHIDFARTSPFGGARPGRVARKRAAAA
GGEEADEE
Sequence of entity 12 (K), FASTA
>3J81_12 eS10 (chains K)
MLIPKEDRKKIYQHLFQEGVLVAKKDFNQPKHEEIDTKNLFVIKALQSLTSKGFVKTQFS
WQYYYYTLTEEGVVYLREYLNLPEHIFPATYLAGQSGDQRPQGKKY
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MET | Methionine | C5 H11 N O2 S | 1 |
| ZN | Zinc ion | Zn | 3 |
| MG | Magnesium ion | Mg | 81 |
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
- 3J80 3.75 Å, CryoEM structure of 40S-eIF1-eIF1A preinitiation complex
- 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…
- 8S8G 4.0 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
Browse structure collections
About this viewer
MolViewer shows 3J81 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.