6HD7: Ribosome-NatA complex
Cryo-EM structure of the ribosome-NatA complex. Determined by electron microscopy at 3.4 Å resolution. Released 19 Dec 2018.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 51
- Atoms
- 141,153
- Mol. weight
- 2146.18 kDa
- Ligands
- 3HE
- Released
- 19 Dec 2018
Explore 6HD7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6HD7 contains 325 α-helices and 305 β-strands across 45 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: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-20 | 9 | |
| α-helix | 27-30 | 4 | |
| β-strand | 33 | 1 | 9 |
| β-strand | 35 | 1 | 10 |
| α-helix | 39-42 | 4 | |
| β-strand | 48 | 1 | 9 |
| β-strand | 57-58 | 2 | 11 |
| β-strand | 67 | 1 | 11 |
| β-strand | 70-74 | 5 | 12 |
| β-strand | 79-88 | 10 | 12 |
| β-strand | 94-99 | 6 | 12 |
| α-helix | 101-103 | 3 | |
| β-strand | 104-105 | 2 | 11 |
| β-strand | 106 | 1 | 10 |
| α-helix | 114-120 | 7 | |
Chain b: 5 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9 | 1 | 13 |
| β-strand | 10-13 | 4 | 14 |
| β-strand | 21-24 | 4 | 14 |
| β-strand | 25-28 | 4 | 15 |
| β-strand | 40-43 | 4 | 15 |
| β-strand | 46 | 1 | 16 |
| α-helix | 49-53 | 5 | |
| α-helix | 60-65 | 6 | |
| β-strand | 70 | 1 | 16 |
| β-strand | 73-76 | 4 | 15 |
| α-helix | 77-79 | 3 | |
| β-strand | 86 | 1 | 13 |
| α-helix | 110-122 | 13 | |
| α-helix | 128-131 | 4 | |
Chain c: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| β-strand | 12 | 1 | 21 |
| β-strand | 14 | 1 | 21 |
| α-helix | 42-45 | 4 | |
| β-strand | 53 | 1 | 95 |
| β-strand | 72-74 | 3 | 22 |
| α-helix | 79-81 | 3 | |
| α-helix | 84-91 | 8 | |
| β-strand | 99 | 1 | 73 |
| β-strand | 101-103 | 3 | 23 |
| β-strand | 111-113 | 3 | 22 |
| β-strand | 124-127 | 4 | 23 |
| β-strand | 129 | 1 | 22 |
| α-helix | 132-140 | 9 | |
| β-strand | 145-147 | 3 | 23 |
Chain C: 3 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-8 | 2 | 17 |
| β-strand | 11-12 | 2 | 18 |
| β-strand | 19-20 | 2 | 18 |
| β-strand | 23-24 | 2 | 17 |
| β-strand | 26-27 | 2 | 19 |
| α-helix | 38-47 | 10 | |
| α-helix | 56-58 | 3 | |
| β-strand | 66-67 | 2 | 20 |
| β-strand | 70-71 | 2 | 19 |
| β-strand | 74 | 1 | 17 |
| β-strand | 82-83 | 2 | 19 |
| β-strand | 87-88 | 2 | 20 |
| α-helix | 103-105 | 3 | |
Chain d: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-16 | 4 | |
| β-strand | 22 | 1 | 103 |
| α-helix | 37-55 | 19 | |
Chain D: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| α-helix | 21-33 | 13 | |
| β-strand | 37 | 1 | 24 |
| α-helix | 38-39 | 2 | |
| β-strand | 47-49 | 3 | 24 |
| β-strand | 55-57 | 3 | 24 |
| β-strand | 63-65 | 3 | 24 |
| α-helix | 78-87 | 10 | |
Chain e: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| β-strand | 24-25 | 2 | 30 |
| α-helix | 27-34 | 8 | |
| β-strand | 41-44 | 4 | 30 |
| α-helix | 50-61 | 12 | |
| β-strand | 67-69 | 3 | 30 |
| α-helix | 74-80 | 7 | |
| β-strand | 89-92 | 4 | 30 |
Chain E: 8 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 28-32 | 5 | |
| α-helix | 34-37 | 4 | |
| β-strand | 42-43 | 2 | 25 |
| β-strand | 44-45 | 2 | 26 |
| α-helix | 50-51 | 2 | |
| β-strand | 58-64 | 7 | 26 |
| β-strand | 71-77 | 7 | 26 |
| β-strand | 79 | 1 | 27 |
| β-strand | 82-83 | 2 | 24 |
| β-strand | 88-89 | 2 | 25 |
| β-strand | 90 | 1 | 28 |
| β-strand | 101-103 | 3 | 28 |
| β-strand | 112-114 | 3 | 28 |
| β-strand | 134-140 | 7 | 28 |
| α-helix | 142-144 | 3 | |
| β-strand | 145-149 | 5 | 28 |
| β-strand | 155-159 | 5 | 28 |
| β-strand | 163-166 | 4 | 28 |
| α-helix | 168 | 1 | |
| β-strand | 169 | 1 | 27 |
| α-helix | 182-189 | 8 | |
| α-helix | 198-200 | 3 | |
| β-strand | 224-225 | 2 | 29 |
| β-strand | 237-238 | 2 | 29 |
37 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 |
|---|
| Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA | 1 | RNA | 3396 | Saccharomyces cerevisiae | |
| 5S rRNA | 3 | RNA | 121 | Saccharomyces cerevisiae | |
| 5.8S rRNA | 4 | RNA | 158 | Saccharomyces cerevisiae | |
| tRNA | A | RNA | 76 | Saccharomyces cerevisiae | |
| P-site tRNA | B | RNA | 77 | Saccharomyces cerevisiae | |
| 60S ribosomal protein L42-A | C | protein | 106 | Saccharomyces cerevisiae | P0CX27 (AlphaFold model) |
| 60S ribosomal protein L43-A | D | protein | 92 | Saccharomyces cerevisiae | P0CX25 (AlphaFold model) |
| 60S ribosomal protein L2-A | E | protein | 254 | Saccharomyces cerevisiae | P0CX45 (AlphaFold model) |
| 60S ribosomal protein L3 | F | protein | 387 | Saccharomyces cerevisiae | P14126 (AlphaFold model) |
| 60S ribosomal protein L4-A | G | protein | 362 | Saccharomyces cerevisiae | P10664 |
| 60S ribosomal protein L5 | H | protein | 297 | Saccharomyces cerevisiae | P26321 |
| 60S ribosomal protein L6-A | I | protein | 176 | Saccharomyces cerevisiae | Q02326 |
39 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>6HD7_1 Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA (chains 1)
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 2 (3), FASTA
>6HD7_2 5S rRNA (chains 3)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U
Sequence of entity 3 (4), FASTA
>6HD7_3 5.8S rRNA (chains 4)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 4 (A), FASTA
>6HD7_4 tRNA (chains A)
GGGUCGUUAGCUCAGUUGGUAGAGCAGUUGACUUUUAAUCAAUUGGUCGCAGGUUCGAAU
CCUGCACGACCCACCA
Sequence of entity 5 (B), FASTA
>6HD7_5 P-site tRNA (chains B)
GGAGCGGUAGUUCAGUCGGUUAGAAUACCUGCCUGUCACGCAGGGGGUCGCGGGUUCGAG
UCCCGUCCGUUCCGCCA
Sequence of entity 6 (C), FASTA
>6HD7_6 60S ribosomal protein L42-A (chains C)
MVNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHK
KAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKGQALQF
Sequence of entity 7 (D), FASTA
>6HD7_7 60S ribosomal protein L43-A (chains D)
MAKRTKKVGITGKYGVRYGSSLRRQVKKLEIQQHARYDCSFCGKKTVKRGAAGIWTCSCC
KKTVAGGAYTVSTAAAATVRSTIRRLREMVEA
Sequence of entity 8 (E), FASTA
>6HD7_8 60S ribosomal protein L2-A (chains E)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD
Sequence of entity 9 (F), FASTA
>6HD7_9 60S ribosomal protein L3 (chains F)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 10 (G), FASTA
>6HD7_10 60S ribosomal protein L4-A (chains G)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 11 (H), FASTA
>6HD7_11 60S ribosomal protein L5 (chains H)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ
Sequence of entity 12 (I), FASTA
>6HD7_12 60S ribosomal protein L6-A (chains I)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 3HE | 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2… | C15 H23 N O4 | 1 |
Primary citation
Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. Knorr, A.G., Schmidt, C., Tesina, P. et al. Nat Struct Mol Biol (2019) 26:35-39. DOI 10.1038/s41594-018-0165-y · PubMed
Other PDB entries of the same protein (UniProt P0CX27 (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…
- 8P8N 2.15 Å, Mouse RPL39 integrated into the yeast 60S ribosomal subunit
- 8PFR 2.15 Å, Mouse RPL39L integrated into the yeast 60S ribosomal subunit
- 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,…
- 8P8U 2.23 Å, Yeast 60S ribosomal subunit
- 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…
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