8CF5: 40S ribosomal protein S24-A
Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin. Determined by electron microscopy at 2.71 Å resolution. Released 20 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 2.71 Å
- Organisms
- Saccharomyces cerevisiae, Escherichia coli
- Chains
- 84
- Atoms
- 208,161
- Mol. weight
- 3309.02 kDa
- Ligands
- SO1, GTP, SPD, MG
- Released
- 20 Sept 2023
Explore 8CF5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8CF5 contains 547 α-helices and 555 β-strands across 75 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 0: 6 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-15 | 10 | 1 |
| β-strand | 20-28 | 9 | 1 |
| α-helix | 37-47 | 11 | |
| β-strand | 55-62 | 8 | 1 |
| α-helix | 63 | 1 | |
| β-strand | 68-76 | 9 | 1 |
| α-helix | 79-85 | 7 | |
| α-helix | 88-94 | 7 | |
| α-helix | 105-115 | 11 | |
| α-helix | 122-134 | 13 | |
Chain 1: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 48-51 | 4 | |
| β-strand | 59-60 | 2 | 7 |
| α-helix | 62-67 | 6 | |
| α-helix | 73-85 | 13 | |
| β-strand | 89-91 | 3 | 7 |
| β-strand | 101-103 | 3 | 7 |
Chain 2: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 17 |
| β-strand | 29-31 | 3 | 17 |
| β-strand | 36-40 | 5 | 18 |
| β-strand | 43 | 1 | 19 |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 20 |
| β-strand | 66 | 1 | 19 |
| β-strand | 69-73 | 5 | 18 |
| α-helix | 75-80 | 6 | |
| α-helix | 91-93 | 3 | |
Chain 3: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| α-helix | 20-22 | 3 | |
| β-strand | 32-36 | 5 | 30 |
| β-strand | 43-47 | 5 | 30 |
| β-strand | 55 | 1 | 31 |
| β-strand | 62 | 1 | 31 |
| β-strand | 79-81 | 3 | 30 |
Chain 4: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-19 | 12 | 38 |
| β-strand | 25-32 | 8 | 38 |
| β-strand | 39-44 | 6 | 38 |
| β-strand | 53-56 | 4 | 38 |
| α-helix | 63-65 | 3 | |
Chain 5: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 30-31 | 2 | 43 |
| α-helix | 33-35 | 3 | |
| β-strand | 38-39 | 2 | 43 |
| α-helix | 40-45 | 6 | |
| α-helix | 47-50 | 4 | |
| β-strand | 53 | 1 | 29 |
Chain 6: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-23 | 3 | |
| α-helix | 33-44 | 12 | |
Chain 7: 0 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-11 | 6 | 51 |
| β-strand | 20-25 | 6 | 52 |
| β-strand | 32-37 | 6 | 52 |
| β-strand | 41-46 | 6 | 52 |
| β-strand | 56-60 | 5 | 52 |
| β-strand | 68-73 | 6 | 53 |
| β-strand | 80-84 | 5 | 53 |
| β-strand | 88-92 | 5 | 53 |
| β-strand | 99-104 | 6 | 53 |
| β-strand | 114 | 1 | 54 |
| β-strand | 122-123 | 2 | 54 |
| β-strand | 133-134 | 2 | 54 |
| β-strand | 153-156 | 4 | 55 |
| β-strand | 169-172 | 4 | 55 |
| β-strand | 199-204 | 6 | 56 |
| β-strand | 210-215 | 6 | 56 |
| β-strand | 219-220 | 2 | 57 |
| β-strand | 221-224 | 4 | 56 |
| β-strand | 229 | 1 | 56 |
| β-strand | 234-235 | 2 | 57 |
| β-strand | 240-244 | 5 | 58 |
| β-strand | 253-256 | 4 | 58 |
| β-strand | 259-262 | 4 | 58 |
| β-strand | 263-265 | 3 | 59 |
| β-strand | 268-270 | 3 | 59 |
| β-strand | 289-294 | 6 | 51 |
| β-strand | 300-305 | 6 | 51 |
| β-strand | 310-316 | 7 | 51 |
67 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 |
|---|
| 40S ribosomal protein S24-A | 0 | protein | 135 | Saccharomyces cerevisiae | P0CX31 (AlphaFold model) |
| 40S ribosomal protein S25-A | 1 | protein | 108 | Saccharomyces cerevisiae | Q3E792 (AlphaFold model) |
| 40S ribosomal protein S26 | 2 | protein | 119 | Saccharomyces cerevisiae | A0A6A5PUG0 |
| 40S ribosomal protein S27-A | 3 | protein | 82 | Saccharomyces cerevisiae | P35997 (AlphaFold model) |
| 40S ribosomal protein S28-A | 4 | protein | 67 | Saccharomyces cerevisiae | Q3E7X9 |
| HLJ1_G0030400.mRNA.1.CDS.1 | 5 | protein | 56 | Saccharomyces cerevisiae | A0A6A5PV92 |
| 40S ribosomal protein S30-A | 6 | protein | 63 | Saccharomyces cerevisiae | P0CX33 |
| Guanine nucleotide-binding protein subunit beta-like protein | 7 | protein | 319 | Saccharomyces cerevisiae | P38011 |
| Ubiquitin-40S ribosomal protein S31 | 8 | protein | 152 | Saccharomyces cerevisiae | A0A6A5PU37 |
| 60S ribosomal protein L16-A | A | protein | 199 | Saccharomyces cerevisiae | P26784 |
| 25S ribosomal RNA | AA | RNA | 3396 | Saccharomyces cerevisiae | |
| Elongation factor 2 | Aa | protein | 842 | Saccharomyces cerevisiae | A0A6A5Q7K2 |
72 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>8CF5_1 40S ribosomal protein S24-A (chains 0)
MSDAVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKAEKDAVSVFGF
RTQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVRYGLAEKVEKASRQQRKQKKNRDKKIFG
TGKRLAKKVARRNAD
Sequence of entity 2 (1), FASTA
>8CF5_2 40S ribosomal protein S25-A (chains 1)
MPPKQQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYV
SVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE
Sequence of entity 3 (2), FASTA
>8CF5_3 40S ribosomal protein S26 (chains 2)
MPKKRASNGRNKKGRGHVKPVRCVNCSKSIPKDKAIKRMAIRNIVEAAAVRDLSEASVYP
EYALPKTYNKLHYCVSCAIHARIVRVRSREDRKNRAPPQRPRFNRENKVSPADAAKKAL
Sequence of entity 4 (3), FASTA
>8CF5_4 40S ribosomal protein S27-A (chains 3)
MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCS
TILCTPTGGKAKLSEGTSFRRK
Sequence of entity 5 (4), FASTA
>8CF5_5 40S ribosomal protein S28-A (chains 4)
MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESE
REARRLR
Sequence of entity 6 (5), FASTA
>8CF5_6 HLJ1_G0030400.mRNA.1.CDS.1 (chains 5)
MAHENVWFSHPRRYGKGSRQCRVCSSHTGLIRKYGLNICRQCFREKANDIGFNKFR
Sequence of entity 7 (6), FASTA
>8CF5_7 40S ribosomal protein S30-A (chains 6)
MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRRMNPGP
SVQ
Sequence of entity 8 (7), FASTA
>8CF5_8 Guanine nucleotide-binding protein subunit beta-like protein (chains 7)
MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRS
FKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKAS
MIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKA
WNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEV
FSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQT
LFAGYTDNVIRVWQVMTAN
Sequence of entity 9 (8), FASTA
>8CF5_9 Ubiquitin-40S ribosomal protein S31 (chains 8)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGGKKRKKKVYTTPKKIKHKHKKVKLAVLSYYKVDAEGKVTKLRRE
CSNPTCGAGVFLANHKDRLYCGKCHSVYKVNA
Sequence of entity 10 (A), FASTA
>8CF5_10 60S ribosomal protein L16-A (chains A)
MSVEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRK
ATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVV
PQALRVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVAS
ANATAAESDVAKQLAALGY
Sequence of entity 11 (AA), FASTA
>8CF5_11 25S ribosomal RNA (chains AA)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU
Sequence of entity 12 (Aa), FASTA
>8CF5_12 Elongation factor 2 (chains Aa)
MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTR
KDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALR
VTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFAR
TVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKM
MDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLL
EKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGP
ADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVP
GKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKV
MKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEI
CLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLA
IENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIK
DSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLA
DPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGF
TGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYD
KL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SO1 | [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-deox… | C27 H42 O8 | 1 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
| SPD | Spermidine | C7 H19 N3 | 11 |
| MG | Magnesium ion | Mg | 241 |
| ZN | Zinc ion | Zn | 8 |
Water and common crystallization additives (K) are not listed.
Primary citation
mRNA reading frame maintenance during eukaryotic ribosome translocation. Milicevic, N., Jenner, L., Myasnikov, A. et al. Nature (2024) 625:393-400. DOI 10.1038/s41586-023-06780-4 · PubMed
Other PDB entries of the same protein (UniProt P0CX31 (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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