8JDK: 60S ribosomal protein L8
Structure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU). Determined by electron microscopy at 2.26 Å resolution. Released 6 Dec 2023.
- Method
- Electron microscopy
- Resolution
- 2.26 Å
- Organism
- Homo sapiens
- Chains
- 80
- Atoms
- 209,567
- Mol. weight
- 3815.8 kDa
- Ligands
- ZN, MAN, MG
- Released
- 6 Dec 2023
Explore 8JDK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8JDK contains 514 α-helices and 544 β-strands across 73 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: 9 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| β-strand | 37-40 | 4 | 8 |
| β-strand | 46-50 | 5 | 8 |
| α-helix | 55-58 | 4 | |
| α-helix | 66-77 | 12 | |
| α-helix | 79-80 | 2 | |
| β-strand | 84-88 | 5 | 8 |
| α-helix | 90-91 | 2 | |
| α-helix | 94-96 | 3 | |
| α-helix | 98-110 | 13 | |
| α-helix | 115-128 | 14 | |
| β-strand | 133-134 | 2 | 9 |
| β-strand | 137-140 | 4 | 10 |
| β-strand | 148-150 | 3 | 10 |
| β-strand | 154-155 | 2 | 9 |
| β-strand | 168-169 | 2 | 9 |
| β-strand | 172-176 | 5 | 10 |
| β-strand | 181-185 | 5 | 10 |
| β-strand | 188-189 | 2 | 9 |
| β-strand | 209-210 | 2 | 11 |
| α-helix | 211-212 | 2 | |
Chain 1: 7 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10 | 1 | 13 |
| β-strand | 27 | 1 | 13 |
| α-helix | 29-32 | 4 | |
| β-strand | 42-43 | 2 | 14 |
| α-helix | 44-47 | 4 | |
| α-helix | 58-66 | 9 | |
| β-strand | 71-72 | 2 | 15 |
| β-strand | 75-76 | 2 | 15 |
| β-strand | 83-84 | 2 | 14 |
| β-strand | 89-91 | 3 | 15 |
| β-strand | 98-100 | 3 | 15 |
| β-strand | 102-103 | 2 | 16 |
| β-strand | 109-110 | 2 | 16 |
| β-strand | 113 | 1 | 15 |
| α-helix | 118-120 | 3 | |
| β-strand | 121-125 | 5 | 17 |
| β-strand | 129-130 | 2 | 18 |
| β-strand | 138-139 | 2 | 18 |
| β-strand | 148 | 1 | 18 |
| β-strand | 159-163 | 5 | 17 |
| β-strand | 169-173 | 5 | 17 |
| β-strand | 180-182 | 3 | 19 |
| α-helix | 186-188 | 3 | |
| β-strand | 192-198 | 7 | 19 |
| β-strand | 207-211 | 5 | 19 |
| β-strand | 217-221 | 5 | 19 |
| α-helix | 222-224 | 3 | |
| α-helix | 248-262 | 15 | |
Chain 2: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 19 | 1 | 30 |
| β-strand | 24 | 1 | 30 |
| α-helix | 36-38 | 3 | |
| α-helix | 62-65 | 4 | |
| α-helix | 68-75 | 8 | |
| α-helix | 80-82 | 3 | |
| α-helix | 86-103 | 18 | |
| α-helix | 108-119 | 12 | |
| β-strand | 123-127 | 5 | 31 |
| β-strand | 136-141 | 6 | 31 |
| α-helix | 143-161 | 19 | |
| α-helix | 169-182 | 14 | |
| α-helix | 188-202 | 15 | |
Chain 3: 4 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 36 |
| β-strand | 12-17 | 6 | 36 |
| α-helix | 22-24 | 3 | |
| β-strand | 30 | 1 | 37 |
| β-strand | 35-36 | 2 | 36 |
| β-strand | 49-52 | 4 | 36 |
| β-strand | 56 | 1 | 36 |
| β-strand | 62 | 1 | 36 |
| β-strand | 63 | 1 | 38 |
| β-strand | 72-77 | 6 | 38 |
| β-strand | 93-98 | 6 | 38 |
| β-strand | 102 | 1 | 37 |
| β-strand | 108-115 | 8 | 36 |
| α-helix | 138-144 | 7 | |
| β-strand | 160-162 | 3 | 39 |
| β-strand | 170-172 | 3 | 39 |
| α-helix | 182-233 | 52 | |
| α-helix | 234-236 | 3 | |
Chain 4: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-24 | 4 | |
| β-strand | 47-49 | 3 | 41 |
| α-helix | 51 | 1 | |
| β-strand | 52 | 1 | 41 |
| α-helix | 53 | 1 | |
| β-strand | 58-64 | 7 | 41 |
| α-helix | 66-68 | 3 | |
| α-helix | 69-73 | 5 | |
| α-helix | 76-86 | 11 | |
| β-strand | 90-96 | 7 | 41 |
| α-helix | 116-117 | 2 | |
| α-helix | 118-120 | 3 | |
| α-helix | 122-133 | 12 | |
| β-strand | 141-142 | 2 | 42 |
| β-strand | 145-146 | 2 | 42 |
| β-strand | 152-157 | 6 | 42 |
| α-helix | 170-181 | 12 | |
| β-strand | 184-188 | 5 | 42 |
Chain 5: 7 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 37-38 | 2 | 46 |
| β-strand | 42-46 | 5 | 46 |
| β-strand | 54-60 | 7 | 46 |
| β-strand | 62 | 1 | 47 |
| β-strand | 66 | 1 | 48 |
| β-strand | 73 | 1 | 48 |
| β-strand | 77 | 1 | 47 |
| β-strand | 78-83 | 6 | 48 |
| α-helix | 88-92 | 5 | |
| β-strand | 95 | 1 | 46 |
| β-strand | 101-104 | 4 | 48 |
| α-helix | 107-117 | 11 | |
| α-helix | 130-136 | 7 | |
| α-helix | 146-149 | 4 | |
| α-helix | 152-154 | 3 | |
| α-helix | 163-168 | 6 | |
| β-strand | 171-175 | 5 | 48 |
| β-strand | 187-189 | 3 | 48 |
| α-helix | 193-205 | 13 | |
Chain 6: 12 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-35 | 14 | |
| α-helix | 40-62 | 23 | |
| α-helix | 64 | 1 | |
| α-helix | 68-84 | 17 | |
| α-helix | 102-106 | 5 | |
| β-strand | 109 | 1 | 55 |
| α-helix | 110-116 | 7 | |
| α-helix | 123-131 | 9 | |
| β-strand | 135-137 | 3 | 56 |
| α-helix | 147 | 1 | |
| β-strand | 148 | 1 | 55 |
| α-helix | 149-150 | 2 | |
| α-helix | 154-156 | 3 | |
| β-strand | 157-159 | 3 | 56 |
| α-helix | 169-171 | 3 | |
| α-helix | 172-182 | 11 | |
Chain 7: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-18 | 14 | |
| β-strand | 20-24 | 5 | 64 |
| β-strand | 31 | 1 | 65 |
| β-strand | 41 | 1 | 65 |
| α-helix | 42-54 | 13 | |
| β-strand | 58-62 | 5 | 64 |
| β-strand | 66-71 | 6 | 64 |
| α-helix | 75-83 | 9 | |
65 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 |
|---|
| mRNA | A | RNA | 14 | Homo sapiens | |
| tRNA (Asp) | B, C | RNA | 75 | Homo sapiens | |
| 28S ribosomal RNA | D | RNA | 5070 | Homo sapiens | |
| 5S ribosomal RNA | E | RNA | 120 | Homo sapiens | |
| 5.8S ribosomal RNA | F | RNA | 156 | Homo sapiens | |
| 60S ribosomal protein L8 | G | protein | 257 | Homo sapiens | P62917 (AlphaFold model) |
| 60S ribosomal protein L3 | H | protein | 403 | Homo sapiens | P39023 (AlphaFold model) |
| 60S ribosomal protein L4 | I | protein | 427 | Homo sapiens | P36578 (AlphaFold model) |
| 60S ribosomal protein L5 | J | protein | 297 | Homo sapiens | P46777 (AlphaFold model) |
| 60S ribosomal protein L6 | K | protein | 288 | Homo sapiens | Q02878 |
| 60S ribosomal protein L7 | L | protein | 248 | Homo sapiens | P18124 |
| 60S ribosomal protein L7a | M | protein | 266 | Homo sapiens | P62424 |
67 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8JDK_1 mRNA (chains A)
UGAUGAUGAUGAUG
Sequence of entity 2 (B, C), FASTA
>8JDK_2 tRNA (Asp) (chains B, C)
UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUXUCACGCGGGAGACCGGGGUUCGAUUC
CCCGACGGGGAGCCA
Sequence of entity 3 (D), FASTA
>8JDK_3 28S ribosomal RNA (chains D)
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
CCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAXGGAUGAACGAGAUUCCCACUGU
CCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGG
AAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGAGAGGUGUA
GAAUAAGUGGGAGGCCCCCGGCGCCCCCCCGGUGUCCCCGCGAGGGGCCCGGGGCGGGGU
CCGCCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCC
GGUGAGGCGGGGGGGCGAGCCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGC
GCGCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCG
GUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCU
CCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCG
UGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAA
AGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUG
AUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGU
UCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUAC
CCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUU
CAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGG
AUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUACGGCAGCGCCG
CGGAGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCUGUCCCCGCCGGCGGGCCGCCC
CCCCCCUCCACGCGCCCCGCGCGCGCGGGAGGGCGCGUGCCCCGCCGCGCGCCGGGACCG
GGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGGCCGGAGAGGCGGCCGC
CCCCUCGCCCGUCACGCACCGCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGAC
GACCUGCUUCUGGGUCGGGG
Sequence of entity 4 (E), FASTA
>8JDK_4 5S ribosomal RNA (chains E)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
Sequence of entity 5 (F), FASTA
>8JDK_5 5.8S ribosomal RNA (chains F)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU
Sequence of entity 6 (G), FASTA
>8JDK_6 60S ribosomal protein L8 (chains G)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 7 (H), FASTA
>8JDK_7 60S ribosomal protein L3 (chains H)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 8 (I), FASTA
>8JDK_8 60S ribosomal protein L4 (chains I)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDKAAAAAAA
LQAKSDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKPAPEKKPAEKKPTT
EEKKPAA
Sequence of entity 9 (J), FASTA
>8JDK_9 60S ribosomal protein L5 (chains J)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMY
KKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 10 (K), FASTA
>8JDK_10 60S ribosomal protein L6 (chains K)
MAGEKVEKPDTKEKKPEAKKVDAGGKVKKGNLKAKKPKKGKPHCSRNPVLVRGIGRYSRS
AMYSRKAMYKRKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTED
VPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLASGLLLVTGPLV
LNRVPLRRTHQKFVIATSTKIDISNVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEKEKY
EITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSVFALTNGIYPHKLVF
Sequence of entity 11 (L), FASTA
>8JDK_11 60S ribosomal protein L7 (chains L)
MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKE
YRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNG
TFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLG
KYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQI
NRLIRRMN
Sequence of entity 12 (M), FASTA
>8JDK_12 60S ribosomal protein L7a (chains M)
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRY
IRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK
KAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVP
YCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGN
VLGPKSVARIAKLEKAKAKELATKLG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 6 |
| MAN | alpha-D-mannopyranose | C6 H12 O6 | 2 |
| MG | Magnesium ion | Mg | 539 |
Primary citation
Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Zhao, X., Ma, D., Ishiguro, K. et al. Cell (2023) 186:5517. DOI 10.1016/j.cell.2023.10.026 · 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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