6GSN: KLLA0F09812p
Structure of a partial yeast 48S preinitiation complex in closed conformation. Determined by electron microscopy at 5.75 Å resolution. Released 26 Jun 2019.
- Method
- Electron microscopy
- Resolution
- 5.75 Å
- Organisms
- Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 47
- Atoms
- 103,798
- Mol. weight
- 1543.51 kDa
- Ligands
- MG, ZN, GCP, MET
- Released
- 26 Jun 2019
Explore 6GSN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6GSN contains 302 α-helices and 393 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, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-22 | 2 | 77 |
| β-strand | 29-30 | 2 | 77 |
| β-strand | 38 | 1 | 78 |
| β-strand | 42-43 | 2 | 79 |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 56 |
| β-strand | 66-67 | 2 | 79 |
| β-strand | 71 | 1 | 78 |
| α-helix | 75-80 | 6 | |
| α-helix | 89-91 | 3 | |
Chain A: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| β-strand | 37-40 | 4 | 10 |
| β-strand | 46-48 | 3 | 10 |
| α-helix | 51-66 | 16 | |
| β-strand | 73-77 | 5 | 11 |
| α-helix | 80-82 | 3 | |
| α-helix | 83-92 | 10 | |
| β-strand | 96-99 | 4 | 11 |
| β-strand | 120-123 | 4 | 11 |
| α-helix | 130-138 | 9 | |
| β-strand | 143-147 | 5 | 11 |
| β-strand | 159-161 | 3 | 11 |
| α-helix | 170-185 | 16 | |
| α-helix | 199-201 | 3 | |
| α-helix | 209-217 | 9 | |
Chain b: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| α-helix | 19 | 1 | |
| β-strand | 32-35 | 4 | 80 |
| β-strand | 44-47 | 4 | 80 |
| α-helix | 53 | 1 | |
| β-strand | 54 | 1 | 81 |
| β-strand | 64-65 | 2 | 81 |
| α-helix | 71 | 1 | |
| β-strand | 72-73 | 2 | 81 |
| β-strand | 79-81 | 3 | 80 |
Chain B: 11 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 24-26 | 3 | |
| β-strand | 27-33 | 7 | 15 |
| β-strand | 42-49 | 8 | 15 |
| α-helix | 57-61 | 5 | |
| β-strand | 65-69 | 5 | 15 |
| α-helix | 71-74 | 4 | |
| α-helix | 77-79 | 3 | |
| β-strand | 82-93 | 12 | 15 |
| β-strand | 95-105 | 11 | 15 |
| α-helix | 107-113 | 7 | |
| α-helix | 119 | 1 | |
| β-strand | 120-128 | 9 | 15 |
| β-strand | 134-142 | 9 | 15 |
| α-helix | 158-175 | 18 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 208-211 | 4 | 15 |
| β-strand | 215-219 | 5 | 15 |
| α-helix | 225-230 | 6 | |
Chain c: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-19 | 12 | 14 |
| β-strand | 25-31 | 7 | 14 |
| β-strand | 39-45 | 7 | 14 |
| β-strand | 53-56 | 4 | 14 |
Chain C: 9 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-52 | 8 | |
| α-helix | 58-64 | 7 | |
| α-helix | 72-77 | 6 | |
| β-strand | 82-94 | 13 | 4 |
| β-strand | 99-110 | 12 | 4 |
| β-strand | 115-123 | 9 | 4 |
| α-helix | 127-140 | 14 | |
| β-strand | 142-143 | 2 | 4 |
| β-strand | 146-147 | 2 | 5 |
| β-strand | 158-159 | 2 | 5 |
| β-strand | 164-167 | 4 | 6 |
| β-strand | 170-173 | 4 | 6 |
| β-strand | 175-176 | 2 | 7 |
| β-strand | 183 | 1 | 7 |
| α-helix | 187-196 | 10 | |
| β-strand | 201-202 | 2 | 7 |
| β-strand | 206 | 1 | 6 |
| α-helix | 212-226 | 15 | |
| α-helix | 237-238 | 2 | |
| α-helix | 241-243 | 3 | |
| α-helix | 244-247 | 4 | |
Chain d: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30 | 1 | 76 |
| β-strand | 39 | 1 | 76 |
| α-helix | 40-45 | 6 | |
| α-helix | 47-50 | 4 | |
| β-strand | 53 | 1 | 55 |
Chain D: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| β-strand | 34-41 | 8 | 8 |
| β-strand | 46-52 | 7 | 8 |
| α-helix | 55-59 | 5 | |
| α-helix | 65-76 | 12 | |
| β-strand | 84-90 | 7 | 8 |
| α-helix | 98-111 | 14 | |
| α-helix | 115-129 | 15 | |
| β-strand | 134-140 | 7 | 9 |
| β-strand | 148-154 | 7 | 9 |
| β-strand | 168-176 | 9 | 9 |
| β-strand | 181-189 | 9 | 9 |
| α-helix | 190-191 | 2 | |
| α-helix | 192-195 | 4 | |
| α-helix | 210-213 | 4 | |
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 |
|---|
| 18S rRNA (1798-mer) | 2 | RNA | 1798 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | |
| KLLA0F09812p | C | protein | 217 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CKL3 (AlphaFold model) |
| KLLA0D08305p | D | protein | 223 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CRK7 (AlphaFold model) |
| KLLA0D10659p | F | protein | 206 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CRA3 (AlphaFold model) |
| KLLA0B08173p | K | protein | 96 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CVZ5 (AlphaFold model) |
| 40S ribosomal protein S12 | M | protein | 118 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CLU4 |
| KLLA0F07843p | P | protein | 117 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CKV4 |
| 40S ribosomal protein S16 | Q | protein | 141 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q875N2 |
| KLLA0B01474p | R | protein | 130 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CWU3 |
| KLLA0B01562p | S | protein | 145 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CWT9 |
| KLLA0A07194p | T | protein | 143 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CXM0 |
| KLLA0F25542p | U | protein | 106 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CIM1 |
35 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>6GSN_1 18S rRNA (1798-MER) (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAA
AUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCU
UGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAA
UUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAAC
GGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAA
GGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGA
UACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGA
ACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUA
UUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGA
CUUUAUGUCGCGCACUGGUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUUG
UGGGUGCAGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAA
AGCUCGAAUAUAUUAGCAUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUU
CUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAG
GUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUU
CAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAAC
CAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUUA
CGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGG
AAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGG
AAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUG
UGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUA
ACGAACGAGACCUUAACCUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUUA
GAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCU
UAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCCG
AGAGGUCUGGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUG
CUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUG
CCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAU
UUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAUU
UAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 2 (C), FASTA
>6GSN_2 KLLA0F09812p (chains C)
GWVPVTKLGRLVKAGKISSIEEIFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTSGKCGSVSVRLIPAPRGSGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKA
AFVAIGNTYGFLTPNLWEVQALTPSPMDVYADYATAS
Sequence of entity 3 (D), FASTA
>6GSN_3 KLLA0D08305p (chains D)
AIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVGEN
GRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAYGV
VRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQGVL
GIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDY
Sequence of entity 4 (F), FASTA
>6GSN_4 KLLA0D10659p (chains F)
FVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASLVDYIQISKPIYVAHTAGRYAN
KRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTLEIINVLTDQNPLQVVVDAIIN
SGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 5 (K), FASTA
>6GSN_5 KLLA0B08173p (chains K)
MLIPKEDRKKIYQHLFQEGVLVAKKDFNQPKHEEIDTKNLFVIKALQSLTSKGFVKTQFS
WQYYYYTLTEEGVVYLREYLNLPEHIFPATYLAGQS
Sequence of entity 6 (M), FASTA
>6GSN_6 40S ribosomal protein S12 (chains M)
IEDALKVVLRTSLVHDGLARGLRESAKALTRGEGQLAVLVESVTEEAISKLVQGLATENN
VPLIKVADAKQLGEWAGLGKIDRDGNARKVVGASVVVVKNWGADTQEREILLEHFSQQ
Sequence of entity 7 (P), FASTA
>6GSN_7 KLLA0F07843p (chains P)
KTYSYKGVDLEKLLEMPTEDFVKLAPARVRRKFARGLSEKPAGLMKKLRAAKLSAPENEK
PAVVRTHLRNMIIVPEMIGSVVGVYNGKVFNQVEIRPEMVGHYLGEFSITYTPVRHG
Sequence of entity 8 (Q), FASTA
>6GSN_8 40S ribosomal protein S16 (chains Q)
TVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVQPEILRFKVYEPLLLVGLDKFAN
IDIRVKVTGGGHVSQVYAIRQAIAKGLVAYHQKFVDEQSKNELKKAFTSYDRTLLIADSR
RPEPKKFGGRGARSRFQKSYR
Sequence of entity 9 (R), FASTA
>6GSN_9 KLLA0B01474p (chains R)
GRVRTKTVKRASKALIEKYYPKLTMDFQTNKRLCDEIATIQSKRLRNKIAGYTTHLMKRI
QKGPVRGISFKLQEEERERKDQYVPDVSALDLSHSNDVLNVDTQTAELVNSLGLKLPLSV
SSVSAVRDRR
Sequence of entity 10 (S), FASTA
>6GSN_10 KLLA0B01562p (chains S)
SLVVQEQGSFQHILRLLNTNVDGNINVVYALTTIRGVGRRYANLVCKKADVDLHKRAGEL
TQEELERIVQIMQNPTHYKIPAWFLNRQKDVNDGKDYHSLANNLESKLRDDLERLKKIRS
HRGIRHFWGLRVRGQHTKTTGRRRA
Sequence of entity 11 (T), FASTA
>6GSN_11 KLLA0A07194p (chains T)
PGVSVRDVPAQDFINNYASFLQRQGKLEVPGYVDIVKTSAGNELPPQDSEGWFYKRAASV
ARHIYLRKQVGVGKLNKLYGGAKNRGVRPHKHVDASGSINRKVLQSLEKLGVVEISPKGG
RRISDNGLRDLDRIAAATLEDEE
Sequence of entity 12 (U), FASTA
>6GSN_12 KLLA0F25542p (chains U)
QEVVIHKIRINLTSTKVKQLENVSANIIKNAETFKLVKKGPVRLPTKVLKISTRKTPNGE
GSKTWDTYEMRIHKRYIDLEAPAHIVKRITQITIEPGVDVEVIIAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 81 |
| ZN | Zinc ion | Zn | 4 |
| GCP | Phosphomethylphosphonic acid guanylate ester | C11 H18 N5 O13 P3 | 1 |
| MET | Methionine | C5 H11 N O2 S | 1 |
Primary citation
Large-scale movement of eIF3 domains during translation initiation modulate start codon selection. Llacer, J.L., Hussain, T., Dong, J. et al. Nucleic Acids Res (2021). DOI 10.1093/nar/gkab908 · PubMed
Other PDB entries of the same protein (UniProt Q6CKL3 (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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