8C01: 40S ribosomal protein S5
Enp1TAP_A population of yeast small ribosomal subunit precursors. Determined by electron microscopy at 2.7 Å resolution. Released 28 Dec 2022.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 31
- Atoms
- 72,685
- Mol. weight
- 1312.97 kDa
- Ligands
- ZN
- Released
- 28 Dec 2022
Explore 8C01 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8C01 contains 273 α-helices and 243 β-strands across 30 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, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 62 |
| β-strand | 8 | 1 | 62 |
| β-strand | 16 | 1 | 63 |
| β-strand | 23 | 1 | 63 |
| β-strand | 32-39 | 8 | 64 |
| β-strand | 45-55 | 11 | 64 |
| α-helix | 57-61 | 5 | |
| α-helix | 65-75 | 11 | |
Chain b: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-20 | 15 | |
| β-strand | 24-27 | 4 | 54 |
| α-helix | 32-43 | 12 | |
| β-strand | 50-53 | 4 | 54 |
| β-strand | 60-64 | 5 | 54 |
| β-strand | 72-74 | 3 | 65 |
| β-strand | 80-81 | 2 | 65 |
| α-helix | 83-85 | 3 | |
| α-helix | 86-93 | 8 | |
| β-strand | 96 | 1 | 66 |
| β-strand | 99 | 1 | 66 |
| β-strand | 101-106 | 6 | 65 |
| β-strand | 109-112 | 4 | 65 |
| α-helix | 113-119 | 7 | |
| β-strand | 123-129 | 7 | 65 |
Chain B: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-34 | 4 | |
| α-helix | 35-37 | 3 | |
| β-strand | 42 | 1 | 1 |
| β-strand | 46 | 1 | 1 |
| α-helix | 56-61 | 6 | |
| α-helix | 83-86 | 4 | |
| α-helix | 89-95 | 7 | |
| α-helix | 101-103 | 3 | |
| α-helix | 107-121 | 15 | |
| α-helix | 129-140 | 12 | |
| β-strand | 144-148 | 5 | 2 |
| β-strand | 157-161 | 5 | 2 |
| α-helix | 164-182 | 19 | |
| α-helix | 190-202 | 13 | |
| α-helix | 209-224 | 16 | |
Chain c: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-22 | 11 | |
| α-helix | 23-25 | 3 | |
| α-helix | 27-34 | 8 | |
| α-helix | 36-39 | 4 | |
| β-strand | 48-60 | 13 | 67 |
| α-helix | 61-62 | 2 | |
| β-strand | 68-76 | 9 | 67 |
| β-strand | 82-86 | 5 | 67 |
| α-helix | 90-95 | 6 | |
| β-strand | 101-106 | 6 | 67 |
| β-strand | 122-127 | 6 | 67 |
| β-strand | 130-131 | 2 | 67 |
| α-helix | 132-136 | 5 | |
Chain C: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-81 | 10 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100-103 | 4 | 9 |
| α-helix | 104-113 | 10 | |
| β-strand | 119-122 | 4 | 9 |
Chain d: 10 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-15 | 10 | 68 |
| α-helix | 16-18 | 3 | |
| β-strand | 20-28 | 9 | 68 |
| α-helix | 37-47 | 11 | |
| α-helix | 52-54 | 3 | |
| β-strand | 55-62 | 8 | 68 |
| α-helix | 63 | 1 | |
| β-strand | 68-76 | 9 | 68 |
| α-helix | 79-85 | 7 | |
| α-helix | 88-93 | 6 | |
| α-helix | 98-100 | 3 | |
| α-helix | 102-104 | 3 | |
| α-helix | 105-115 | 11 | |
| α-helix | 123-131 | 9 | |
Chain e: 22 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 215-221 | 7 | |
| α-helix | 228-230 | 3 | |
| α-helix | 231-235 | 5 | |
| α-helix | 236-238 | 3 | |
| α-helix | 242-249 | 8 | |
| α-helix | 251-253 | 3 | |
| α-helix | 256-263 | 8 | |
| α-helix | 274-278 | 5 | |
| α-helix | 279-283 | 5 | |
| α-helix | 284-293 | 10 | |
| α-helix | 298-300 | 3 | |
| α-helix | 301-309 | 9 | |
| α-helix | 314-317 | 4 | |
| α-helix | 318-322 | 5 | |
| α-helix | 332-342 | 11 | |
| α-helix | 349-358 | 10 | |
| α-helix | 369-375 | 7 | |
| α-helix | 376-378 | 3 | |
| α-helix | 384-391 | 8 | |
| α-helix | 415-424 | 10 | |
| α-helix | 436-444 | 9 | |
| α-helix | 455-459 | 5 | |
Chain E: 10 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-17 | 2 | 11 |
| β-strand | 20-21 | 2 | 11 |
| α-helix | 30-33 | 4 | |
| α-helix | 34-36 | 3 | |
| α-helix | 39-46 | 8 | |
| α-helix | 52-65 | 14 | |
| β-strand | 76-78 | 3 | 12 |
| α-helix | 83 | 1 | |
| β-strand | 84 | 1 | 13 |
| α-helix | 85 | 1 | |
| α-helix | 87-89 | 3 | |
| β-strand | 93-97 | 5 | 12 |
| β-strand | 102-106 | 5 | 12 |
| α-helix | 109-111 | 3 | |
| β-strand | 115 | 1 | 13 |
| α-helix | 116-119 | 4 | |
| α-helix | 124-126 | 3 | |
22 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 precursor | 2 | RNA | 1804 | Saccharomyces cerevisiae | |
| 40S ribosomal protein S5 | B | protein | 225 | Saccharomyces cerevisiae | P26783 (AlphaFold model) |
| 40S ribosomal protein S17-A | C | protein | 136 | Saccharomyces cerevisiae | P02407 (AlphaFold model) |
| 40S ribosomal protein S15 | E | protein | 142 | Saccharomyces cerevisiae | Q01855 (AlphaFold model) |
| 40S ribosomal protein S16-A | F | protein | 143 | Saccharomyces cerevisiae | P0CX51 (AlphaFold model) |
| 40S ribosomal protein S18-A | H | protein | 146 | Saccharomyces cerevisiae | P0CX55 |
| 40S ribosomal protein S19-A | I | protein | 144 | Saccharomyces cerevisiae | P07280 |
| 40S ribosomal protein S25-A | K | protein | 108 | Saccharomyces cerevisiae | Q3E792 |
| 40S ribosomal protein S28-A | L | protein | 67 | Saccharomyces cerevisiae | Q3E7X9 |
| 40S ribosomal protein S0-A | P | protein | 252 | Saccharomyces cerevisiae | P32905 |
| 40S ribosomal protein S1-A | Q | protein | 255 | Saccharomyces cerevisiae | P33442 |
| 40S ribosomal protein S2 | R | protein | 254 | Saccharomyces cerevisiae | P25443 |
19 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>8C01_1 18S rRNA precursor (chains 2)
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
AAGA
Sequence of entity 2 (B), FASTA
>8C01_2 40S ribosomal protein S5 (chains B)
MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD
YVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDI
INVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAR
EAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 3 (C), FASTA
>8C01_3 40S ribosomal protein S17-A (chains C)
MGRVRTKTVKRASKALIERYYPKLTLDFQTNKRLCDEIATIQSKRLRNKIAGYTTHLMKR
IQKGPVRGISFKLQEEERERKDQYVPEVSALDLSRSNGVLNVDNQTSDLVKSLGLKLPLS
VINVSAQRDRRYRKRV
Sequence of entity 4 (E), FASTA
>8C01_4 40S ribosomal protein S15 (chains E)
MSQAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKL
RAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFS
ITYTPVRHGRAGATTSRFIPLK
Sequence of entity 5 (F), FASTA
>8C01_5 40S ribosomal protein S16-A (chains F)
MSAVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKF
SNIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIAD
SRRPEPKKFGGKGARSRFQKSYR
Sequence of entity 6 (H), FASTA
>8C01_6 40S ribosomal protein S18-A (chains H)
MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGE
LTQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIR
AHRGIRHFWGLRVRGQHTKTTGRRRA
Sequence of entity 7 (I), FASTA
>8C01_7 40S ribosomal protein S19-A (chains I)
MPGVSVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAAS
VARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKG
GRRISENGQRDLDRIAAQTLEEDE
Sequence of entity 8 (K), FASTA
>8C01_8 40S ribosomal protein S25-A (chains K)
MPPKQQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYV
SVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE
Sequence of entity 9 (L), FASTA
>8C01_9 40S ribosomal protein S28-A (chains L)
MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESE
REARRLR
Sequence of entity 10 (P), FASTA
>8C01_10 40S ribosomal protein S0-A (chains P)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW
Sequence of entity 11 (Q), FASTA
>8C01_11 40S ribosomal protein S1-A (chains Q)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV
Sequence of entity 12 (R), FASTA
>8C01_12 40S ribosomal protein S2 (chains R)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors. Poll, G., Griesenbeck, J., Tschochner, H. et al. PLoS One (2023) 18:e0283698-e0283698. DOI 10.1371/journal.pone.0283698 · PubMed
Other PDB entries of the same protein (UniProt P26783 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
- 8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
- 8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
- 8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
- 8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
- 8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
- 8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
- 7ZW0 2.4 Å, FAP-80S Complex - Rotated state
- 8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing
- 8T2Z 2.4 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
- 8T2X 2.46 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger…
- 8CIV 2.47 Å, Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2…
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