5DC3: 40S ribosomal protein S0-A
Complex of yeast 80S ribosome with non-modified eIF5A. Determined by X-ray diffraction at 3.25 Å resolution. Released 1 Jun 2016.
- Method
- X-ray diffraction
- Resolution
- 3.25 Å
- Organisms
- Saccharomyces cerevisiae S288c, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae
- Chains
- 163
- Atoms
- 404,042
- Mol. weight
- 6288.66 kDa
- Ligands
- ZN
- Released
- 1 Jun 2016
Explore 5DC3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5DC3 contains 956 α-helices and 1,074 β-strands across 154 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 c0: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-17 | 13 | |
| β-strand | 20-21 | 2 | 186 |
| α-helix | 39-50 | 12 | |
| β-strand | 51 | 1 | 187 |
| β-strand | 53 | 1 | 187 |
| β-strand | 55-59 | 5 | 186 |
| β-strand | 64-68 | 5 | 186 |
| α-helix | 70-79 | 10 | |
Chain C0: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-18 | 14 | |
| β-strand | 20-24 | 5 | 173 |
| α-helix | 39-50 | 12 | |
| β-strand | 55-58 | 4 | 173 |
| β-strand | 63-68 | 6 | 173 |
| α-helix | 69 | 1 | |
| α-helix | 70-80 | 11 | |
| α-helix | 82-83 | 2 | |
Chain c1: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 39 | 1 | 196 |
| β-strand | 42 | 1 | 196 |
| α-helix | 43-45 | 3 | |
| β-strand | 70-77 | 8 | 197 |
| β-strand | 84-94 | 11 | 197 |
| α-helix | 95-97 | 3 | |
| β-strand | 99-110 | 12 | 197 |
| β-strand | 122-127 | 6 | 197 |
| β-strand | 137-142 | 6 | 197 |
Chain C1: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 39 | 1 | 180 |
| β-strand | 42 | 1 | 180 |
| α-helix | 46-50 | 5 | |
| β-strand | 70-77 | 8 | 181 |
| β-strand | 83-94 | 12 | 181 |
| β-strand | 99-110 | 12 | 181 |
| β-strand | 122-127 | 6 | 181 |
| β-strand | 137-142 | 6 | 181 |
| α-helix | 149-152 | 4 | |
Chain c2: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-31 | 4 | |
| β-strand | 41-43 | 3 | 209 |
| α-helix | 46-52 | 7 | |
| β-strand | 60-62 | 3 | 209 |
| α-helix | 70-78 | 9 | |
| α-helix | 94-99 | 6 | |
| β-strand | 120-123 | 4 | 209 |
| α-helix | 131-133 | 3 | |
| α-helix | 135-141 | 7 | |
Chain C2: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-36 | 10 | |
| β-strand | 41-43 | 3 | 189 |
| α-helix | 45-53 | 9 | |
| β-strand | 59-61 | 3 | 189 |
| α-helix | 70-78 | 9 | |
| α-helix | 94-100 | 7 | |
| β-strand | 121-123 | 3 | 189 |
| α-helix | 131-141 | 11 | |
Chain c3: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-42 | 14 | |
| α-helix | 47-57 | 11 | |
| β-strand | 58 | 1 | 48 |
| α-helix | 71-78 | 8 | |
| α-helix | 86-102 | 17 | |
| α-helix | 111-131 | 21 | |
| α-helix | 143-145 | 3 | |
| α-helix | 146-150 | 5 | |
Chain C3: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-43 | 14 | |
| α-helix | 47-56 | 10 | |
| α-helix | 63-66 | 4 | |
| α-helix | 71-77 | 7 | |
| α-helix | 86-104 | 19 | |
| α-helix | 109-131 | 23 | |
| α-helix | 143-150 | 8 | |
144 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 ribosomal RNA | 2, 6 | RNA | 1800 | Saccharomyces cerevisiae S288c | |
| 40S ribosomal protein S0-A | S0, s0 | protein | 251 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32905 (AlphaFold model) |
| 40S ribosomal protein S1-A | S1, s1 | protein | 254 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33442 (AlphaFold model) |
| 40S ribosomal protein S2 | S2, s2 | protein | 253 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25443 (AlphaFold model) |
| 40S ribosomal protein S3 | S3, s3 | protein | 239 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P05750 (AlphaFold model) |
| 40S ribosomal protein S4-A | S4, s4 | protein | 260 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX35 |
| 40S ribosomal protein S5 | S5, s5 | protein | 224 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26783 |
| 40S ribosomal protein S6-A | S6, s6 | protein | 236 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX37 |
| 40S ribosomal protein S7-A | S7, s7 | protein | 189 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26786 |
| 40S ribosomal protein S8-A | S8, s8 | protein | 200 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX39 |
| 40S ribosomal protein S9-A | S9, s9 | protein | 196 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | O13516 |
| 40S ribosomal protein S10-A | C0 | protein | 105 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q08745 |
73 more molecules are not listed.
Sequence of entity 1 (2, 6), FASTA
>5DC3_1 18S ribosomal RNA (chains 2, 6)
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
Sequence of entity 2 (S0, s0), FASTA
>5DC3_2 40S ribosomal protein S0-A (chains S0, s0)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEATE
WAEENADNVEW
Sequence of entity 3 (S1, s1), FASTA
>5DC3_3 40S ribosomal protein S1-A (chains S1, s1)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEKG
KKVTGFKDEVLETV
Sequence of entity 4 (S2, s2), FASTA
>5DC3_4 40S ribosomal protein S2 (chains S2, s2)
SAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHSL
PVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEV
AGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVAS
PAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPLD
IYSDEASAQKKRF
Sequence of entity 5 (S3, s3), FASTA
>5DC3_5 40S ribosomal protein S3 (chains S3, s3)
VALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGE
NGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYG
VVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGV
LGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA
Sequence of entity 6 (S4, s4), FASTA
>5DC3_6 40S ribosomal protein S4-A (chains S4, s4)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQGL
Sequence of entity 7 (S5, s5), FASTA
>5DC3_7 40S ribosomal protein S5 (chains S5, s5)
SDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDY
VQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDII
NVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGARE
AAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 8 (S6, s6), FASTA
>5DC3_8 40S ribosomal protein S6-A (chains S6, s6)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA
Sequence of entity 9 (S7, s7), FASTA
>5DC3_9 40S ribosomal protein S7-A (chains S7, s7)
SAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIF
VPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAV
HDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQI
VFEIPSETH
Sequence of entity 10 (S8, s8), FASTA
>5DC3_10 40S ribosomal protein S8-A (chains S8, s8)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK
Sequence of entity 11 (S9, s9), FASTA
>5DC3_11 40S ribosomal protein S9-A (chains S9, s9)
PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKS
VHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKA
EASGEAADEADEADEE
Sequence of entity 12 (C0), FASTA
>5DC3_12 40S ribosomal protein S10-A (chains C0)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERNPTQRPQRRY
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 16 |
Primary citation
Crystal Structure of Hypusine-Containing Translation Factor eIF5A Bound to a Rotated Eukaryotic Ribosome. Melnikov, S., Mailliot, J., Shin, B.S. et al. J Mol Biol (2016) 428:3570-3576. DOI 10.1016/j.jmb.2016.05.011 · PubMed
Other PDB entries of the same protein (UniProt P32905 (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…
- 8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 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
- 8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 7ZW0 2.4 Å, FAP-80S Complex - Rotated state
- 8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing
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