3JAP: US2
Structure of a partial yeast 48S preinitiation complex in closed conformation. Determined by electron microscopy at 4.9 Å resolution. Released 12 Aug 2015.
- Method
- Electron microscopy
- Resolution
- 4.9 Å
- Organisms
- Kluyveromyces lactis, synthetic construct, Saccharomyces cerevisiae
- Chains
- 47
- Atoms
- 98,333
- Mol. weight
- 1546.9 kDa
- Ligands
- GCP, MET, ZN, MG
- Released
- 12 Aug 2015
Explore 3JAP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3JAP contains 286 α-helices and 333 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: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-19 | 2 | |
| β-strand | 20-22 | 3 | 7 |
| β-strand | 29-31 | 3 | 7 |
| β-strand | 37-43 | 7 | 8 |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 69 |
| β-strand | 66-72 | 7 | 8 |
| α-helix | 75-81 | 7 | |
| α-helix | 86-88 | 3 | |
Chain A: 7 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| β-strand | 37-40 | 4 | 5 |
| β-strand | 46-48 | 3 | 5 |
| α-helix | 50-66 | 17 | |
| β-strand | 73-77 | 5 | 6 |
| α-helix | 80-82 | 3 | |
| α-helix | 83-92 | 10 | |
| β-strand | 96-99 | 4 | 6 |
| β-strand | 120-123 | 4 | 6 |
| α-helix | 130-138 | 9 | |
| β-strand | 143-145 | 3 | 6 |
| β-strand | 159 | 1 | 6 |
| α-helix | 169-185 | 17 | |
| α-helix | 199-201 | 3 | |
Chain b: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 97 |
| α-helix | 12-17 | 6 | |
| α-helix | 19 | 1 | |
| β-strand | 32-36 | 5 | 10 |
| β-strand | 43-47 | 5 | 10 |
| β-strand | 54 | 1 | 11 |
| β-strand | 64-65 | 2 | 11 |
| α-helix | 71 | 1 | |
| β-strand | 72-73 | 2 | 11 |
| β-strand | 78-81 | 4 | 10 |
Chain B: 7 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-26 | 3 | |
| β-strand | 27-33 | 7 | 9 |
| β-strand | 42-49 | 8 | 9 |
| β-strand | 65-69 | 5 | 9 |
| α-helix | 77-79 | 3 | |
| β-strand | 82-93 | 12 | 9 |
| β-strand | 95-105 | 11 | 9 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-127 | 8 | 9 |
| β-strand | 134-142 | 9 | 9 |
| α-helix | 158-175 | 18 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 208-211 | 4 | 9 |
| β-strand | 215-219 | 5 | 9 |
| α-helix | 226-230 | 5 | |
Chain c: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-19 | 12 | 15 |
| β-strand | 25-32 | 8 | 15 |
| β-strand | 39-45 | 7 | 15 |
| β-strand | 53-56 | 4 | 15 |
Chain C: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-52 | 8 | |
| α-helix | 58-64 | 7 | |
| α-helix | 72-77 | 6 | |
| β-strand | 84-94 | 11 | 12 |
| β-strand | 99-110 | 12 | 12 |
| β-strand | 115-123 | 9 | 12 |
| α-helix | 126-140 | 15 | |
| β-strand | 142-143 | 2 | 12 |
| β-strand | 146-147 | 2 | 13 |
| β-strand | 158-159 | 2 | 13 |
| β-strand | 163-166 | 4 | 14 |
| β-strand | 171-176 | 6 | 14 |
| α-helix | 177-178 | 2 | |
| β-strand | 183-184 | 2 | 14 |
| α-helix | 187-196 | 10 | |
| β-strand | 201-203 | 3 | 14 |
| β-strand | 206 | 1 | 14 |
| α-helix | 212-224 | 13 | |
| α-helix | 237-238 | 2 | |
| α-helix | 241-243 | 3 | |
| α-helix | 244-247 | 4 | |
Chain d: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31 | 1 | 18 |
| α-helix | 33-35 | 3 | |
| β-strand | 38 | 1 | 18 |
| α-helix | 41-46 | 6 | |
| α-helix | 47-49 | 3 | |
| β-strand | 53 | 1 | 93 |
Chain D: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| β-strand | 34-41 | 8 | 16 |
| β-strand | 46-52 | 7 | 16 |
| α-helix | 56-59 | 4 | |
| α-helix | 64-77 | 14 | |
| β-strand | 84-90 | 7 | 16 |
| α-helix | 98-111 | 14 | |
| α-helix | 115-129 | 15 | |
| β-strand | 134-141 | 8 | 17 |
| β-strand | 147-154 | 8 | 17 |
| α-helix | 162-164 | 3 | |
| β-strand | 168-176 | 9 | 17 |
| β-strand | 181-189 | 9 | 17 |
| α-helix | 192-195 | 4 | |
| α-helix | 210-212 | 3 | |
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 |
|---|
| Met-tRNAi (U31:A39 variant) | 1 | RNA | 75 | Kluyveromyces lactis | |
| 18S rRNA | 2 | RNA | 1781 | Kluyveromyces lactis | |
| mRNA | 3 | RNA | 25 | synthetic construct | |
| 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 |
35 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>3JAP_1 Met-tRNAi (U31:A39 variant) (chains 1)
AGCGCCGUGGCGCAGUGGAAGCGCGCAGGUCUCAUAAACCUGAUGUCCUCGGAUCGAAAC
CGAGCGGCGCUACCA
Sequence of entity 2 (2), FASTA
>3JAP_2 18S rRNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAA
AUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCU
UGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAA
UUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAAC
GGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAA
GGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGA
UACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGA
ACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUA
UUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGG
UUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUUGUGGGUGCAGGCGAACCA
GGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAAAGCUCGAAUAUAUUAGC
AUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUG
AUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUU
AUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAA
AGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACU
AGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUU
UGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAC
CACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAG
ACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGG
CCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAAC
CUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUUAGAGGGACUAUCGGUUUC
AAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGC
ACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCCGAGAGGUCUGGGUAAUCU
UGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUU
CCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGC
CCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUUUGCUUAGAGAAGGGGG
CAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAUUUAGAGGAACUAAAAGUC
GUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 3 (3), FASTA
>3JAP_3 mRNA (chains 3)
GGAAUCUCUCUCUAUGCUCUCUCUC
Sequence of entity 4 (A), FASTA
>3JAP_4 uS2 (chains A)
MSLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLA
ARIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALPDRTQPWAIMPDLYFYRNPEEIEQQTAEEEAVASGEQTEEAVDATEEQTEAA
EWAEEGQAQEEEWN
Sequence of entity 5 (B), FASTA
>3JAP_5 eS1 (chains B)
MAVGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDS
LKGRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNST
LAQLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHGEASAEEK
GKKVAGFKDEILETV
Sequence of entity 6 (C), FASTA
>3JAP_6 uS5 (chains C)
MSAPQAQGQQAPRRGGFGGANRGGRGGRRGGRRDQEEKGWVPVTKLGRLVKAGKISSIEE
IFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGI
KTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTSGKCGSVSVRLIPAPRG
SGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKAAFVAIGNTYGFLTPNLWEVQAL
TPSPMDVYADYATASKKKL
Sequence of entity 7 (D), FASTA
>3JAP_7 uS3 (chains D)
MVAIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVG
ENGRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQG
VLGIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDYRPTEPVEAAESA
Sequence of entity 8 (E), FASTA
>3JAP_8 eS4 (chains E)
MARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEAS
YKLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKL
VYVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPK
GKGIKLTISEERDRRRAQHGL
Sequence of entity 9 (F), FASTA
>3JAP_9 uS7 (chains F)
MSEHEAQVEVEVQEDFEVVQEFVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASL
VDYIQISKPIYVAHTAGRYANKRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTL
EIINVLTDQNPLQVVVDAIINSGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIG
AREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 10 (G), FASTA
>3JAP_10 eS6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEVRKRRASSLKA
Sequence of entity 11 (H), FASTA
>3JAP_11 eS7 (chains H)
MSDPQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAV
FVPVPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQ
IVFEIPSETH
Sequence of entity 12 (I), FASTA
>3JAP_12 eS8 (chains I)
MGISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRI
ETGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQS
LGKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRC
DGYILEGEELAFYLRRLTAKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GCP | Phosphomethylphosphonic acid guanylate ester | C11 H18 N5 O13 P3 | 1 |
| MET | Methionine | C5 H11 N O2 S | 1 |
| ZN | Zinc ion | Zn | 4 |
| MG | Magnesium ion | Mg | 81 |
Primary citation
Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. Llacer, J.L., Hussain, T., Marler, L. et al. Mol Cell (2015) 59:399-412. DOI 10.1016/j.molcel.2015.06.033 · 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…
- 3J81 4.0 Å, CryoEM structure of a partial yeast 48S preinitiation complex
Browse structure collections
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