8IFD: Dibekacin-added human 80S ribosome
Dibekacin-added human 80S ribosome. Determined by electron microscopy at 2.59 Å resolution. Released 14 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 2.59 Å
- Organism
- Homo sapiens
- Chains
- 80
- Atoms
- 217,933
- Mol. weight
- 3825.79 kDa
- Ligands
- 84D, MG, ZN
- Released
- 14 Feb 2024
Explore 8IFD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8IFD contains 543 α-helices and 550 β-strands across 76 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 1D: 11 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-5 | 2 | |
| α-helix | 10-12 | 3 | |
| α-helix | 29-32 | 4 | |
| α-helix | 34-38 | 5 | |
| β-strand | 40-49 | 10 | 17 |
| β-strand | 58-64 | 7 | 17 |
| β-strand | 71-77 | 7 | 17 |
| α-helix | 78 | 1 | |
| β-strand | 79 | 1 | 18 |
| β-strand | 83 | 1 | 19 |
| β-strand | 87-91 | 5 | 17 |
| β-strand | 101-103 | 3 | 17 |
| α-helix | 104-106 | 3 | |
| α-helix | 108 | 1 | |
| β-strand | 112-113 | 2 | 20 |
| β-strand | 116 | 1 | 21 |
| β-strand | 120 | 1 | 22 |
| β-strand | 122 | 1 | 22 |
| β-strand | 126 | 1 | 21 |
| β-strand | 134-140 | 7 | 20 |
| β-strand | 145-149 | 5 | 20 |
| β-strand | 155-159 | 5 | 20 |
| β-strand | 163-165 | 3 | 17 |
| β-strand | 166 | 1 | 20 |
| β-strand | 169 | 1 | 18 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-190 | 9 | |
| α-helix | 201-203 | 3 | |
| β-strand | 224-225 | 2 | 23 |
| α-helix | 229-230 | 2 | |
| β-strand | 237-238 | 2 | 23 |
Chain 1E: 21 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| α-helix | 14-16 | 3 | |
| α-helix | 32-35 | 4 | |
| α-helix | 40-41 | 2 | |
| β-strand | 42-43 | 2 | 26 |
| β-strand | 45-59 | 15 | 27 |
| β-strand | 71-80 | 10 | 27 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-95 | 12 | 28 |
| β-strand | 98-106 | 9 | 28 |
| α-helix | 107 | 1 | |
| α-helix | 112-115 | 4 | |
| α-helix | 116-118 | 3 | |
| α-helix | 133-137 | 5 | |
| α-helix | 140-156 | 17 | |
| β-strand | 159-165 | 7 | 28 |
| α-helix | 168-170 | 3 | |
| α-helix | 178-179 | 2 | |
| β-strand | 180-184 | 5 | 28 |
| β-strand | 185-186 | 2 | 26 |
| α-helix | 190-200 | 11 | |
| β-strand | 204-205 | 2 | 28 |
| α-helix | 207-209 | 3 | |
| β-strand | 216-222 | 7 | 27 |
| α-helix | 223-225 | 3 | |
| β-strand | 227-229 | 3 | 29 |
| α-helix | 231-234 | 4 | |
| α-helix | 237-241 | 5 | |
| β-strand | 270-272 | 3 | 29 |
| β-strand | 276-288 | 13 | 27 |
| β-strand | 292-293 | 2 | 30 |
| β-strand | 297-298 | 2 | 30 |
| α-helix | 300-302 | 3 | |
| α-helix | 316 | 1 | |
| β-strand | 320 | 1 | 31 |
| β-strand | 324 | 1 | 31 |
| β-strand | 330-334 | 5 | 27 |
| β-strand | 344-349 | 6 | 27 |
| β-strand | 365-368 | 4 | 27 |
| α-helix | 382-388 | 7 | |
| α-helix | 393-402 | 10 | |
Chain 1F: 22 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-11 | 5 | 35 |
| α-helix | 12 | 1 | |
| β-strand | 17-23 | 7 | 35 |
| α-helix | 24-25 | 2 | |
| α-helix | 26-29 | 4 | |
| α-helix | 34-44 | 11 | |
| α-helix | 49-51 | 3 | |
| β-strand | 64-65 | 2 | 36 |
| β-strand | 78-79 | 2 | 36 |
| β-strand | 90 | 1 | 36 |
| α-helix | 100-101 | 2 | |
| α-helix | 117-131 | 15 | |
| α-helix | 134-140 | 7 | |
| β-strand | 152-154 | 3 | 35 |
| α-helix | 156-160 | 5 | |
| α-helix | 164-174 | 11 | |
| α-helix | 177-186 | 10 | |
| β-strand | 188-189 | 2 | 37 |
| α-helix | 193-197 | 5 | |
| β-strand | 201-202 | 2 | 37 |
| β-strand | 208-210 | 3 | 35 |
| α-helix | 217-221 | 5 | |
| β-strand | 228-229 | 2 | 35 |
| α-helix | 237-240 | 4 | |
| β-strand | 250-253 | 4 | 35 |
| α-helix | 254-264 | 11 | |
| α-helix | 279-282 | 4 | |
| α-helix | 289-293 | 5 | |
| α-helix | 296-301 | 6 | |
| α-helix | 303-305 | 3 | |
| α-helix | 311-313 | 3 | |
| α-helix | 322-328 | 7 | |
| α-helix | 331-367 | 37 | |
Chain 1G: 18 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-15 | 6 | |
| α-helix | 21-25 | 5 | |
| α-helix | 30-37 | 8 | |
| α-helix | 38-40 | 3 | |
| β-strand | 50-55 | 6 | 40 |
| β-strand | 60-66 | 7 | 40 |
| β-strand | 73-79 | 7 | 40 |
| α-helix | 80-85 | 6 | |
| α-helix | 95-113 | 19 | |
| α-helix | 134-135 | 2 | |
| α-helix | 139-142 | 4 | |
| β-strand | 143 | 1 | 41 |
| β-strand | 145-147 | 3 | 40 |
| α-helix | 158-169 | 12 | |
| β-strand | 172 | 1 | 41 |
| α-helix | 177-179 | 3 | |
| β-strand | 183-184 | 2 | 42 |
| β-strand | 189-190 | 2 | 42 |
| α-helix | 193-199 | 7 | |
| α-helix | 202-214 | 13 | |
| α-helix | 217-222 | 6 | |
| α-helix | 224-227 | 4 | |
| α-helix | 228-230 | 3 | |
| α-helix | 236-249 | 14 | |
| α-helix | 268-272 | 5 | |
| α-helix | 273-293 | 21 | |
Chain 1H: 11 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 49-51 | 3 | 45 |
| β-strand | 54-55 | 2 | 45 |
| α-helix | 59-66 | 8 | |
| β-strand | 91-94 | 4 | 46 |
| β-strand | 105-108 | 4 | 46 |
| α-helix | 111-113 | 3 | |
| α-helix | 121-126 | 6 | |
| α-helix | 133-135 | 3 | |
| α-helix | 137-138 | 2 | |
| β-strand | 148-152 | 5 | 47 |
| β-strand | 160 | 1 | 48 |
| β-strand | 161-163 | 3 | 47 |
| β-strand | 164-167 | 4 | 49 |
| α-helix | 172 | 1 | |
| β-strand | 173-175 | 3 | 49 |
| α-helix | 179-182 | 4 | |
| β-strand | 187-189 | 3 | 49 |
| α-helix | 191-193 | 3 | |
| β-strand | 194-200 | 7 | 47 |
| α-helix | 214-217 | 4 | |
| α-helix | 244-263 | 20 | |
| α-helix | 267-272 | 6 | |
| β-strand | 274 | 1 | 48 |
Chain 20: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 11-24 | 14 | |
| α-helix | 52-66 | 15 | |
| β-strand | 70 | 1 | 61 |
| α-helix | 72-79 | 8 | |
| β-strand | 81-83 | 3 | 62 |
| α-helix | 89-90 | 2 | |
| β-strand | 91-93 | 3 | 62 |
| α-helix | 97-110 | 14 | |
| β-strand | 113-115 | 3 | 61 |
| β-strand | 121-123 | 3 | 61 |
| α-helix | 125-143 | 19 | |
Chain 21: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-26 | 9 | 66 |
| α-helix | 29-45 | 17 | |
| β-strand | 50 | 1 | 66 |
| α-helix | 51-53 | 3 | |
| β-strand | 54-65 | 12 | 66 |
| β-strand | 78-93 | 16 | 66 |
| α-helix | 99-102 | 4 | |
| β-strand | 110-115 | 6 | 66 |
Chain 2a: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-24 | 5 | 59 |
| β-strand | 30-34 | 5 | 59 |
| α-helix | 37-39 | 3 | |
| α-helix | 41-42 | 2 | |
| β-strand | 43 | 1 | 60 |
| α-helix | 44 | 1 | |
| β-strand | 52 | 1 | 60 |
| α-helix | 53 | 1 | |
| α-helix | 63-66 | 4 | |
| α-helix | 69-71 | 3 | |
| α-helix | 84-110 | 27 | |
68 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 |
|---|
| 28S ribosomal RNA | 1A | RNA | 5070 | Homo sapiens | |
| 5S ribosomal RNA | 1B | RNA | 121 | Homo sapiens | |
| 5.8S ribosomal RNA | 1C | RNA | 157 | Homo sapiens | |
| 60S ribosomal protein L8 | 1D | protein | 257 | Homo sapiens | P62917 (AlphaFold model) |
| 60S ribosomal protein L3 | 1E | protein | 403 | Homo sapiens | P39023 (AlphaFold model) |
| 60S ribosomal protein L4 | 1F | protein | 427 | Homo sapiens | P36578 (AlphaFold model) |
| 60S ribosomal protein L5 | 1G | protein | 297 | Homo sapiens | P46777 (AlphaFold model) |
| 60S ribosomal protein L6 | 1H | protein | 288 | Homo sapiens | Q02878 |
| 60S ribosomal protein L7 | 2A | protein | 248 | Homo sapiens | P18124 |
| 60S ribosomal protein L7a | 2B | protein | 266 | Homo sapiens | P62424 |
| 60S ribosomal protein L9 | 2C | protein | 192 | Homo sapiens | P32969 |
| 60S ribosomal protein L10-like | 2D | protein | 214 | Homo sapiens | Q96L21 |
68 more molecules are not listed.
Sequence of entity 1 (1A), FASTA
>8IFD_1 28S ribosomal RNA (chains 1A)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAG
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGC
CGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCG
GUAGCGGCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCA
GCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAA
CAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAA
CCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGC
GGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCCCCCCGUUCCUCCCGACCCCU
CCACCCGCCCUCCCUUCCCCCGCCGCCCCUCCUCCUCCUCCCCGGAGGGGGCGGGCUCCG
GCGGGUGCGGGGGUGGGCGGGCGGGGCCGGGGGUGGGGUCGGCGGGGGACCGUCCCCCGA
CCGGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCG
GGACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGGGGGCCCCGUCCGUCCGUCCGUC
CGUCCUCCUCCUCCCCCGUCUCCGCCCCCCGGCCCCGCGUCCUCCCUCGGGAGGGCGCGC
GGGUCGGGGCGGCGGCGGCGGCGGCGGUGGCGGCGGCGGCGGCGGCGGCGGGACCGAAAC
CCCCCCCGAGUGUUACAGCCCCCCCGGCAGCAGCACUCGCCGAAUCCCGGGGCCGAGGGA
GCGAGACCCGUCGCCGCGCUCUCCCCCCUCCCGGCGCCCACCCCCGCGGGGAAUCCCCCG
CGAGGGGGGUCUCCCCCGCGGGGGCGCGCCGGCGUCUCCUCGUGGGGGGGCCGGGCCACC
CCUCCCACGGCGCGACCGCUCUCCCACCCCUCCUCCCCGCGCCCCCGCCCCGGCGACGGG
GGGGGUGCCGCGCGCGGGUCGGGGGGCGGGGCGGACUGUCCCCAGUGCGCCCCGGGCGGG
UCGCGCCGUCGGGCCCGGGGGAGGUUCUCUCGGGGCCACGCGCGCGUCCCCCGAAGAGGG
GGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCCACCCGACCCGUCUU
GAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCGCACGAAAGCCGCCG
UGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGGAUCCCGAGGCCUCU
CCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCA
CGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGA
GGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGUCGUCCGACCUGGGU
AUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAG
GAUAGCUGGCGCUCUCGCAGACCCGACGCACCCCCGCCACGCAGUUUUAUCCGGUAAAGC
GAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGU
AAGAAGCCCGGCUCGCUGGCGUGGAGCCGGGCGUGGAAUGCGAGUGCCUAGUGGGCCACU
UUUGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGC
CGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAU
GGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGA
AAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGA
CGGGAGCGGCGGCGGCGGCGCGCGCGCGCGCGCGUGUGGUGUGCGUCGGAGGGCGGCGGC
GGCGGCGGCGGCGGGGGUGUGGGGUCCUUCCCCCGCCCCCCCCCCCACGCCUCCUCCCCU
CCUCCCGCCCACGCCCCGCUCCCCGCCCCCGGAGCCCCGCGGACGCUACGCCGCGACGAG
UAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGC
AGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGG
AGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGA
GCGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGAGUC
GGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGU
AACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUG
AAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCG
UCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGG
UGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUC
UGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAU
AAGGAUUGGCUCUAAGGGCUGGGUCGGUCGGGCUGGGGCGCGAAGCGGGGCUGGGCGCGC
GCCGCGGCUGGACGAGGCGCCGCCGCCCCCCCCACGCCCGGGGCACCCCCCUCGCGGCCC
UCCCCCGCCCCACCCCGCGCGCGCCGCUCGCUCCCUCCCCGCCCCGCGCCCUCUCUCUCU
CUCUCUCCCCCGCUCCCCGUCCUCCCCCCUCCCCGGGGGAGCGCCGCGUGGGGGCGGCGG
CGGGGGGAGAAGGGUCGGGGCGGCAGGGGCCGGCGGCGGCCCGCCGCGGGGCCCCGGCGG
CGGGGGCACGGUCCCCCGCGAGGGGGGCCCGGGCACCCGGGGGGCCGGCGGCGGCGGCGA
CUCUGGACGCGAGCCGGGCCCUUCCCGUGGAUCGCCCCAGCUGCGGCGGGCGUCGCGGCC
GCCCCCGGGGAGCCCGGCGGGCGCCGGCGCGCCCCCCCCCCCACCCCACGUCUCGUCGCG
CGCGCGUCCGCUGGGGGCGGGGAGCGGUCGGGCGGCGGCGGUCGGCGGGCGGCGGGGCGG
GGCGGUUCGUCCCCCCGCCCUACCCCCCCGGCCCCGUCCGCCCCCCGUUCCCCCCUCCUC
CUCGGCGCGCGGCGGCGGCGGCGGCAGGCGGCGGAGGGGCCGCGGGCCGGUCCCCCCCGC
CGGGUCCGCCCCCGGGGCCGCGGUUCCGCGCGGCGCCUCGCCUCGGCCGGCGCCUAGCAG
CCGACUUAGAACUGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGC
GAAGGCCCGCGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAG
UGAAGAAAUUCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAG
CCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGU
CCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGG
AAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGAGAGGUGUA
GAAUAAGUGGGAGGCCCCCGGCGCCCCCCCGGUGUCCCCGCGAGGGGCCCGGGGCGGGGU
CCGCCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCC
GGUGAGGCGGGGGGGCGAGCCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGC
GCGCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCG
GUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCU
CCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCG
UGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAA
AGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUG
AUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGU
UCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUAC
CCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUU
CAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGG
AUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUACGGCAGCGCCG
CGGAGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCUGUCCCCGCCGGCGGGCCGCCC
CCCCCCUCCACGCGCCCCGCGCGCGCGGGAGGGCGCGUGCCCCGCCGCGCGCCGGGACCG
GGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGGCCGGAGAGGCGGCCGC
CCCCUCGCCCGUCACGCACCGCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGAC
GACCUGCUUCUGGGUCGGGG
Sequence of entity 2 (1B), FASTA
>8IFD_2 5S ribosomal RNA (chains 1B)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
U
Sequence of entity 3 (1C), FASTA
>8IFD_3 5.8S ribosomal RNA (chains 1C)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCUU
Sequence of entity 4 (1D), FASTA
>8IFD_4 60S ribosomal protein L8 (chains 1D)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 5 (1E), FASTA
>8IFD_5 60S ribosomal protein L3 (chains 1E)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 6 (1F), FASTA
>8IFD_6 60S ribosomal protein L4 (chains 1F)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDKAAAAAAA
LQAKSDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKPAPEKKPAEKKPTT
EEKKPAA
Sequence of entity 7 (1G), FASTA
>8IFD_7 60S ribosomal protein L5 (chains 1G)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMY
KKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 8 (1H), FASTA
>8IFD_8 60S ribosomal protein L6 (chains 1H)
MAGEKVEKPDTKEKKPEAKKVDAGGKVKKGNLKAKKPKKGKPHCSRNPVLVRGIGRYSRS
AMYSRKAMYKRKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTED
VPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLASGLLLVTGPLV
LNRVPLRRTHQKFVIATSTKIDISNVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEKEKY
EITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSVFALTNGIYPHKLVF
Sequence of entity 9 (2A), FASTA
>8IFD_9 60S ribosomal protein L7 (chains 2A)
MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKE
YRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNG
TFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLG
KYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQI
NRLIRRMN
Sequence of entity 10 (2B), FASTA
>8IFD_10 60S ribosomal protein L7a (chains 2B)
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRY
IRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK
KAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVP
YCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGN
VLGPKSVARIAKLEKAKAKELATKLG
Sequence of entity 11 (2C), FASTA
>8IFD_11 60S ribosomal protein L9 (chains 2C)
MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 12 (2D), FASTA
>8IFD_12 60S ribosomal protein L10-like (chains 2D)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLGGHMVSDEYEQL
SSEALEAARICANKYMVKSCGRDGFHMRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNEEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAKKCLIPDGCGVKYVPSHGPLDKWRVLHS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 84D | Dibekacin | C18 H37 N5 O8 | 24 |
| MG | Magnesium ion | Mg | 397 |
| ZN | Zinc ion | Zn | 4 |
Primary citation
Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. Tomono, J., Asano, K., Chiashi, T. et al. J Biochem (2024) 175:587-598. DOI 10.1093/jb/mvae002 · PubMed
Other PDB entries of the same protein (UniProt P62917 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
- 29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
- 8QYX 1.78 Å, Human 60S ribosomal subunit
- 8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
- 9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
- 8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
- 9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
- 29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
- 9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
- 9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
- 9PBE 2.19 Å, In situ human 80S ribosome (composite map)
- 29IX 2.2 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. NT-2 added to purified…
Browse structure collections
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