8YOP: Human 80S ribosome with 4 um Tigecycline
Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline. Determined by electron microscopy at 2.2 Å resolution. Released 10 Jul 2024.
- Method
- Electron microscopy
- Resolution
- 2.2 Å
- Organism
- Homo sapiens
- Chains
- 82
- Atoms
- 218,499
- Mol. weight
- 3863.97 kDa
- Ligands
- ZN, MG
- Released
- 10 Jul 2024
Explore 8YOP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8YOP contains 549 α-helices and 554 β-strands across 78 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 La: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 42-48 | 7 | |
| α-helix | 65-68 | 4 | |
| β-strand | 72-74 | 3 | 19 |
| α-helix | 75-81 | 7 | |
| α-helix | 84-92 | 9 | |
| β-strand | 97-98 | 2 | 102 |
| α-helix | 99 | 1 | |
| β-strand | 100-102 | 3 | 20 |
| α-helix | 103-106 | 4 | |
| β-strand | 110-112 | 3 | 19 |
| β-strand | 123-126 | 4 | 20 |
| β-strand | 128-129 | 2 | 19 |
| α-helix | 131-140 | 10 | |
| β-strand | 143-146 | 4 | 20 |
Chain LA: 10 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-5 | 2 | |
| α-helix | 8-12 | 5 | |
| α-helix | 30-32 | 3 | |
| α-helix | 34-38 | 5 | |
| β-strand | 41-49 | 9 | 24 |
| β-strand | 58-64 | 7 | 24 |
| β-strand | 71-77 | 7 | 24 |
| α-helix | 78 | 1 | |
| β-strand | 79 | 1 | 25 |
| β-strand | 83 | 1 | 26 |
| β-strand | 86-90 | 5 | 24 |
| β-strand | 101-103 | 3 | 24 |
| β-strand | 112-114 | 3 | 24 |
| β-strand | 116-117 | 2 | 27 |
| β-strand | 124-126 | 3 | 27 |
| β-strand | 134-140 | 7 | 24 |
| α-helix | 142-144 | 3 | |
| β-strand | 145-149 | 5 | 24 |
| β-strand | 155-159 | 5 | 24 |
| β-strand | 163-166 | 4 | 24 |
| β-strand | 169 | 1 | 25 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-192 | 11 | |
| α-helix | 201-203 | 3 | |
| β-strand | 224-225 | 2 | 28 |
| α-helix | 229-230 | 2 | |
| β-strand | 237-238 | 2 | 28 |
Chain Lb: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-18 | 7 | |
| α-helix | 22-26 | 5 | |
| α-helix | 37-48 | 12 | |
| α-helix | 49-51 | 3 | |
| α-helix | 54-73 | 20 | |
| α-helix | 92-100 | 9 | |
| α-helix | 106-117 | 12 | |
Chain LB: 18 helices, 21 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 | 35 |
| β-strand | 45-60 | 16 | 36 |
| β-strand | 68 | 1 | 36 |
| β-strand | 70-80 | 11 | 36 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-95 | 12 | 37 |
| β-strand | 98-106 | 9 | 37 |
| α-helix | 107 | 1 | |
| α-helix | 112-118 | 7 | |
| α-helix | 131-138 | 8 | |
| α-helix | 140-156 | 17 | |
| β-strand | 159-165 | 7 | 37 |
| α-helix | 178-179 | 2 | |
| β-strand | 180-184 | 5 | 37 |
| β-strand | 185-186 | 2 | 35 |
| α-helix | 190-199 | 10 | |
| β-strand | 203-205 | 3 | 37 |
| α-helix | 207-210 | 4 | |
| β-strand | 216-222 | 7 | 36 |
| α-helix | 223-225 | 3 | |
| β-strand | 227-229 | 3 | 38 |
| α-helix | 231-234 | 4 | |
| α-helix | 237-241 | 5 | |
| β-strand | 270-272 | 3 | 38 |
| β-strand | 276-288 | 13 | 36 |
| β-strand | 292 | 1 | 39 |
| β-strand | 298 | 1 | 39 |
| α-helix | 316 | 1 | |
| β-strand | 320 | 1 | 40 |
| β-strand | 324 | 1 | 40 |
| β-strand | 330-334 | 5 | 36 |
| β-strand | 343-349 | 7 | 36 |
| β-strand | 365-368 | 4 | 36 |
| α-helix | 382-389 | 8 | |
| α-helix | 393-402 | 10 | |
Chain Lc: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-24 | 15 | |
| β-strand | 26-29 | 4 | 41 |
| α-helix | 31-40 | 10 | |
| β-strand | 45-49 | 5 | 41 |
| α-helix | 54-67 | 14 | |
| β-strand | 70-74 | 5 | 41 |
| α-helix | 78-84 | 7 | |
| β-strand | 93-98 | 6 | 41 |
Chain LC: 21 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-11 | 5 | 43 |
| α-helix | 12 | 1 | |
| β-strand | 17-23 | 7 | 43 |
| α-helix | 24-25 | 2 | |
| α-helix | 34-47 | 14 | |
| β-strand | 65 | 1 | 44 |
| β-strand | 78 | 1 | 44 |
| β-strand | 90 | 1 | 44 |
| α-helix | 99-101 | 3 | |
| α-helix | 117-132 | 16 | |
| α-helix | 134-140 | 7 | |
| β-strand | 152-154 | 3 | 43 |
| α-helix | 164-173 | 10 | |
| α-helix | 177-186 | 10 | |
| β-strand | 188-189 | 2 | 45 |
| α-helix | 190-191 | 2 | |
| α-helix | 193-195 | 3 | |
| β-strand | 201-202 | 2 | 45 |
| β-strand | 208-210 | 3 | 43 |
| α-helix | 217-220 | 4 | |
| β-strand | 228-229 | 2 | 43 |
| α-helix | 237-240 | 4 | |
| β-strand | 250-253 | 4 | 43 |
| α-helix | 254-263 | 10 | |
| α-helix | 279-282 | 4 | |
| α-helix | 289-293 | 5 | |
| α-helix | 296-301 | 6 | |
| α-helix | 303-305 | 3 | |
| α-helix | 311-314 | 4 | |
| α-helix | 316-317 | 2 | |
| α-helix | 322-328 | 7 | |
| α-helix | 332-365 | 34 | |
Chain Ld: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-28 | 7 | 46 |
| α-helix | 29-32 | 4 | |
| α-helix | 38-40 | 3 | |
| α-helix | 41-56 | 16 | |
| β-strand | 62-64 | 3 | 46 |
| α-helix | 66-72 | 7 | |
| α-helix | 73-75 | 3 | |
| β-strand | 83-92 | 10 | 46 |
| β-strand | 102-108 | 7 | 46 |
| α-helix | 117-119 | 3 | |
| β-strand | 120-121 | 2 | 46 |
Chain LD: 17 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-14 | 5 | |
| α-helix | 21-25 | 5 | |
| α-helix | 30-37 | 8 | |
| α-helix | 38-40 | 3 | |
| α-helix | 41-43 | 3 | |
| β-strand | 50-55 | 6 | 48 |
| β-strand | 60-66 | 7 | 48 |
| β-strand | 73-79 | 7 | 48 |
| α-helix | 83-85 | 3 | |
| α-helix | 95-113 | 19 | |
| α-helix | 134-135 | 2 | |
| α-helix | 139-142 | 4 | |
| β-strand | 143 | 1 | 49 |
| β-strand | 145-147 | 3 | 48 |
| α-helix | 158-169 | 12 | |
| β-strand | 172 | 1 | 49 |
| β-strand | 183-184 | 2 | 50 |
| β-strand | 189-190 | 2 | 50 |
| α-helix | 192-199 | 8 | |
| α-helix | 202-214 | 13 | |
| α-helix | 217-222 | 6 | |
| α-helix | 224-228 | 5 | |
| α-helix | 236-249 | 14 | |
| α-helix | 268-272 | 5 | |
| α-helix | 273-293 | 21 | |
70 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 rRNA | L5 | RNA | 5070 | Homo sapiens | |
| 5S rRNA | L7 | RNA | 121 | Homo sapiens | |
| 5.8S rRNA | L8 | RNA | 157 | Homo sapiens | |
| 60S ribosomal protein L8 | LA | protein | 257 | Homo sapiens | P62917 (AlphaFold model) |
| 60S ribosomal protein L3 | LB | protein | 403 | Homo sapiens | P39023 (AlphaFold model) |
| 60S ribosomal protein L4 | LC | protein | 427 | Homo sapiens | P36578 (AlphaFold model) |
| 60S ribosomal protein L5 | LD | protein | 297 | Homo sapiens | P46777 (AlphaFold model) |
| 60S ribosomal protein L6 | LE | protein | 288 | Homo sapiens | Q02878 |
| 60S ribosomal protein L7 | LF | protein | 248 | Homo sapiens | P18124 |
| 60S ribosomal protein L7a | LG | protein | 266 | Homo sapiens | P62424 |
| 60S ribosomal protein L9 | LH | protein | 192 | Homo sapiens | P32969 |
| Large ribosomal subunit protein uL16 | LI | protein | 214 | Homo sapiens | P27635 |
70 more molecules are not listed.
Sequence of entity 1 (L5), FASTA
>8YOP_1 28S rRNA (chains L5)
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 (L7), FASTA
>8YOP_2 5S rRNA (chains L7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
U
Sequence of entity 3 (L8), FASTA
>8YOP_3 5.8S rRNA (chains L8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCUU
Sequence of entity 4 (LA), FASTA
>8YOP_4 60S ribosomal protein L8 (chains LA)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 5 (LB), FASTA
>8YOP_5 60S ribosomal protein L3 (chains LB)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 6 (LC), FASTA
>8YOP_6 60S ribosomal protein L4 (chains LC)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDKAAAAAAA
LQAKSDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKPAPEKKPAEKKPTT
EEKKPAA
Sequence of entity 7 (LD), FASTA
>8YOP_7 60S ribosomal protein L5 (chains LD)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMY
KKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 8 (LE), FASTA
>8YOP_8 60S ribosomal protein L6 (chains LE)
MAGEKVEKPDTKEKKPEAKKVDAGGKVKKGNLKAKKPKKGKPHCSRNPVLVRGIGRYSRS
AMYSRKAMYKRKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTED
VPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLASGLLLVTGPLV
LNRVPLRRTHQKFVIATSTKIDISNVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEKEKY
EITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSVFALTNGIYPHKLVF
Sequence of entity 9 (LF), FASTA
>8YOP_9 60S ribosomal protein L7 (chains LF)
MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKE
YRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNG
TFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLG
KYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQI
NRLIRRMN
Sequence of entity 10 (LG), FASTA
>8YOP_10 60S ribosomal protein L7a (chains LG)
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRY
IRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK
KAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVP
YCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGN
VLGPKSVARIAKLEKAKAKELATKLG
Sequence of entity 11 (LH), FASTA
>8YOP_11 60S ribosomal protein L9 (chains LH)
MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 12 (LI), FASTA
>8YOP_12 Large ribosomal subunit protein uL16 (chains LI)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPSRGPLDKWRALHS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
| MG | Magnesium ion | Mg | 255 |
Primary citation
Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline. Li, X., Wang, M., Denk, T. et al. Nat Commun (2024) 15:5481-5481. DOI 10.1038/s41467-024-49797-7 · 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…
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