8OHD: 60S ribosomal subunit
60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native). Determined by electron microscopy at 3.1 Å resolution. Released 21 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Homo sapiens
- Chains
- 50
- Atoms
- 146,745
- Mol. weight
- 2803.34 kDa
- Ligands
- ZN, MG
- Released
- 21 Feb 2024
Explore 8OHD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OHD contains 433 α-helices and 371 β-strands across 47 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: 36 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-42 | 13 | |
| β-strand | 48-49 | 2 | 11 |
| β-strand | 55-57 | 3 | 11 |
| α-helix | 59-73 | 15 | |
| β-strand | 76-78 | 3 | 12 |
| α-helix | 79-86 | 8 | |
| α-helix | 90-103 | 14 | |
| β-strand | 107-110 | 4 | 12 |
| β-strand | 113-116 | 4 | 12 |
| α-helix | 117-134 | 18 | |
| β-strand | 136-138 | 3 | 13 |
| α-helix | 139-146 | 8 | |
| α-helix | 150-160 | 11 | |
| β-strand | 161 | 1 | 14 |
| β-strand | 165 | 1 | 14 |
| β-strand | 168-169 | 2 | 13 |
| β-strand | 176-178 | 3 | 13 |
| α-helix | 180-196 | 17 | |
| β-strand | 201-202 | 2 | 15 |
| α-helix | 203-210 | 8 | |
| α-helix | 214-227 | 14 | |
| β-strand | 233-235 | 3 | 15 |
| β-strand | 238 | 1 | 16 |
| β-strand | 243-245 | 3 | 15 |
| α-helix | 247-264 | 18 | |
| β-strand | 266-268 | 3 | 17 |
| α-helix | 269-275 | 7 | |
| α-helix | 280-287 | 8 | |
| β-strand | 294-295 | 2 | 17 |
| β-strand | 299-301 | 3 | 17 |
| α-helix | 303-319 | 17 | |
| β-strand | 322-324 | 3 | 18 |
| α-helix | 335-346 | 12 | |
| α-helix | 347-349 | 3 | |
| β-strand | 356 | 1 | 18 |
| β-strand | 362-364 | 3 | 18 |
| α-helix | 366-374 | 9 | |
| α-helix | 377-388 | 12 | |
| α-helix | 417-426 | 10 | |
| α-helix | 480-488 | 9 | |
| α-helix | 495-520 | 26 | |
| α-helix | 521-525 | 5 | |
| α-helix | 531-558 | 28 | |
| α-helix | 566-573 | 8 | |
| α-helix | 574-578 | 5 | |
| α-helix | 579-592 | 14 | |
| α-helix | 605-614 | 10 | |
| α-helix | 617-631 | 15 | |
| α-helix | 636-648 | 13 | |
| α-helix | 658-678 | 21 | |
| α-helix | 682-698 | 17 | |
| α-helix | 709-716 | 8 | |
| α-helix | 722-746 | 25 | |
| α-helix | 758-763 | 6 | |
| α-helix | 764-768 | 5 | |
| α-helix | 769-783 | 15 | |
Chain B: 23 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-6 | 5 | |
| α-helix | 8 | 1 | |
| β-strand | 9-12 | 4 | 20 |
| α-helix | 14-17 | 4 | |
| α-helix | 30-45 | 16 | |
| α-helix | 52-58 | 7 | |
| α-helix | 65-73 | 9 | |
| α-helix | 96-104 | 9 | |
| α-helix | 109-120 | 12 | |
| α-helix | 121-125 | 5 | |
| α-helix | 126-167 | 42 | |
| α-helix | 175-181 | 7 | |
| α-helix | 182-185 | 4 | |
| α-helix | 186-199 | 14 | |
| α-helix | 202-215 | 14 | |
| α-helix | 225-232 | 8 | |
| β-strand | 237 | 1 | 21 |
| α-helix | 238-242 | 5 | |
| β-strand | 342 | 1 | 21 |
| α-helix | 347-371 | 25 | |
| α-helix | 374-376 | 3 | |
| α-helix | 377-384 | 8 | |
| α-helix | 388-391 | 4 | |
| α-helix | 395-413 | 19 | |
| α-helix | 415-425 | 11 | |
| α-helix | 427-492 | 66 | |
| β-strand | 499-502 | 4 | 20 |
Chain C: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 119-191 | 73 | |
| α-helix | 193-195 | 3 | |
| β-strand | 197-202 | 6 | 23 |
| α-helix | 209-211 | 3 | |
| α-helix | 212-225 | 14 | |
| β-strand | 228-230 | 3 | 24 |
| α-helix | 231-238 | 8 | |
| α-helix | 242-255 | 14 | |
| β-strand | 260-262 | 3 | 24 |
| β-strand | 267-270 | 4 | 24 |
| α-helix | 273-286 | 14 | |
| β-strand | 289-290 | 2 | 11 |
| α-helix | 291-301 | 11 | |
Chain D: 2 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 23 |
| β-strand | 10 | 1 | 29 |
| β-strand | 18-24 | 7 | 23 |
| β-strand | 28 | 1 | 30 |
| α-helix | 29-40 | 12 | |
| β-strand | 48-50 | 3 | 29 |
| β-strand | 56 | 1 | 29 |
| β-strand | 62 | 1 | 30 |
| α-helix | 63-70 | 8 | |
| β-strand | 73 | 1 | 23 |
| β-strand | 75-77 | 3 | 29 |
Chain K: 10 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-5 | 4 | 32 |
| α-helix | 13-16 | 4 | |
| β-strand | 17-19 | 3 | 33 |
| β-strand | 24-27 | 4 | 33 |
| α-helix | 32-38 | 7 | |
| α-helix | 39-43 | 5 | |
| β-strand | 48-51 | 4 | 33 |
| β-strand | 53 | 1 | 34 |
| β-strand | 56 | 1 | 34 |
| β-strand | 64-65 | 2 | 35 |
| β-strand | 69-72 | 4 | 35 |
| α-helix | 78-87 | 10 | |
| β-strand | 93-96 | 4 | 35 |
| α-helix | 104-107 | 4 | |
| β-strand | 108-110 | 3 | 36 |
| β-strand | 114-117 | 4 | 36 |
| α-helix | 123-133 | 11 | |
| β-strand | 136-139 | 4 | 36 |
| β-strand | 142 | 1 | 37 |
| β-strand | 145 | 1 | 37 |
| α-helix | 148-151 | 4 | |
| β-strand | 153-154 | 2 | 38 |
| β-strand | 159-161 | 3 | 38 |
| α-helix | 167-177 | 11 | |
| β-strand | 181-183 | 3 | 38 |
| β-strand | 186 | 1 | 39 |
| β-strand | 190 | 1 | 39 |
| α-helix | 193-196 | 4 | |
| β-strand | 197-199 | 3 | 32 |
| β-strand | 204-207 | 4 | 32 |
| α-helix | 212-222 | 11 | |
Chain La: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 7-10 | 4 | |
| α-helix | 42-48 | 7 | |
| α-helix | 65-68 | 4 | |
| β-strand | 72-74 | 3 | 40 |
| α-helix | 78-81 | 4 | |
| α-helix | 84-92 | 9 | |
| β-strand | 97-98 | 2 | 99 |
| β-strand | 100-102 | 3 | 41 |
| α-helix | 103-106 | 4 | |
| β-strand | 110-112 | 3 | 40 |
| β-strand | 123-126 | 4 | 41 |
| β-strand | 128-129 | 2 | 40 |
| α-helix | 131-139 | 9 | |
| β-strand | 143-146 | 4 | 41 |
Chain LA: 11 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-5 | 2 | |
| α-helix | 14-16 | 3 | |
| α-helix | 29-32 | 4 | |
| α-helix | 34-38 | 5 | |
| β-strand | 40-49 | 10 | 42 |
| α-helix | 57 | 1 | |
| β-strand | 58-64 | 7 | 42 |
| β-strand | 71-77 | 7 | 42 |
| β-strand | 79 | 1 | 43 |
| β-strand | 83 | 1 | 44 |
| β-strand | 87-91 | 5 | 42 |
| β-strand | 101-103 | 3 | 42 |
| α-helix | 108 | 1 | |
| β-strand | 112-114 | 3 | 42 |
| β-strand | 116 | 1 | 45 |
| β-strand | 126 | 1 | 45 |
| β-strand | 134-140 | 7 | 42 |
| β-strand | 145-149 | 5 | 42 |
| β-strand | 155-159 | 5 | 42 |
| β-strand | 163-166 | 4 | 42 |
| β-strand | 169 | 1 | 43 |
| β-strand | 171 | 1 | 46 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-190 | 9 | |
| α-helix | 201-203 | 3 | |
| α-helix | 206-208 | 3 | |
| β-strand | 224-225 | 2 | 47 |
| α-helix | 229-230 | 2 | |
| β-strand | 237-238 | 2 | 47 |
Chain Lb: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-19 | 8 | |
| β-strand | 22 | 1 | 2 |
| α-helix | 23-26 | 4 | |
| α-helix | 37-48 | 12 | |
| α-helix | 49-53 | 5 | |
| α-helix | 54-74 | 21 | |
| α-helix | 92-100 | 9 | |
| α-helix | 106-117 | 12 | |
39 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 | 5 | RNA | 5070 | Homo sapiens | |
| 5S rRNA | 7 | RNA | 121 | Homo sapiens | |
| 5.8S rRNA | 8 | RNA | 157 | Homo sapiens | |
| E3 UFM1-protein ligase 1 | A | protein | 794 | Homo sapiens | O94874 (AlphaFold model) |
| CDK5 regulatory subunit-associated protein 3 | B | protein | 506 | Homo sapiens | Q96JB5 (AlphaFold model) |
| DDRGK domain-containing protein 1 | C | protein | 314 | Homo sapiens | Q96HY6 (AlphaFold model) |
| Ubiquitin-fold modifier 1 | D | protein | 85 | Homo sapiens | P61960 (AlphaFold model) |
| Eukaryotic translation initiation factor 6 | K | protein | 245 | Homo sapiens | P56537 |
| 60S ribosomal protein L8 | LA | protein | 257 | Homo sapiens | P62917 |
| 60S ribosomal protein L3 | LB | protein | 403 | Homo sapiens | P39023 |
| 60S ribosomal protein L4 | LC | protein | 427 | Homo sapiens | P36578 |
| 60S ribosomal protein L5 | LD | protein | 297 | Homo sapiens | P46777 |
38 more molecules are not listed.
Sequence of entity 1 (5), FASTA
>8OHD_1 28S rRNA (chains 5)
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
GGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGGCUGGAAAGGCGGCCGC
CCCCUCGCCCGUCACGCACCGCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGAC
GACCUGCUUCUGGGUCGGGG
Sequence of entity 2 (7), FASTA
>8OHD_2 5S rRNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
U
Sequence of entity 3 (8), FASTA
>8OHD_3 5.8S rRNA (chains 8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCUU
Sequence of entity 4 (A), FASTA
>8OHD_4 E3 UFM1-protein ligase 1 (chains A)
MADAWEEIRRLAADFQRAQFAEATQRLSERNCIEIVNKLIAQKQLEVVHTLDGKEYITPA
QISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEKHVQLVLGQLIDENYL
DRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRIISGHIDLDNRGVIFTE
AFVARHKARIRGLFSAITRPTAVNSLISKYGFQEQLLYSVLEELVNSGRLRGTVVGGRQD
KAVFVPDIYSRTQSTWVDSFFRQNGYLEFDALSRLGIPDAVSYIKKRYKTTQLLFLKAAC
VGQGLVDQVEASVEEAISSGTWVDIAPLLPTSLSVEDAAILLQQVMRAFSKQASTVVFSD
TVVVSEKFINDCTELFRELMHQKAEKEMKNNPVHLITEEDLKQISTLESVSTSKKDKKDE
RRRKATEGSGSMRGGGGGNAREYKIKKVKKKGRKDDDSDDESQSSHTGKKKPEISFMFQD
EIEDFLRKHIQDAPEEFISELAEYLIKPLNKTYLEVVRSVFMSSTTSASGTGRKRTIKDL
QEEVSNLYNNIRLFEKGMKFFADDTQAALTKHLLKSVCTDITNLIFNFLASDLMMAVDDP
AAITSEIRKKILSKLSEETKVALTKLHNSLNEKSIEDFISCLDSAAEACDIMVKRGDKKR
ERQILFQHRQALAEQLKVTEDPALILHLTSVLLFQFSTHSMLHAPGRCVPQIIAFLNSKI
PEDQHALLVKYQGLVVKQLVSQSKKTGQGDYPLNNELDKEQEDVASTTRKELQELSSSIK
DLVLKSRKSSVTEE
Sequence of entity 5 (B), FASTA
>8OHD_5 CDK5 regulatory subunit-associated protein 3 (chains B)
MEDHQHVPIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDMPESEEIAQLLSG
SYIHYFHCLRILDLLKGTEASTKNIFGRYSSQRMKDWQEIIALYEKDNTYLVELSSLLVR
NVNYEIPSLKKQIAKCQQLQQEYSRKEEECQAGAAEMREQFYHSCKQYGITGENVRGELL
ALVKDLPSQLAEIGAAAQQSLGEAIDVYQASVGFVCESPTEQVLPMLRFVQKRGNSTVYE
WRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEGTDSGISAEAAGIDWGIFPES
DSKDPGGDGIDWGDDAVALQITVLEAGTQAPEGVARGPDALTLLEYTETRNQFLDELMEL
EIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEKMVTMVSVLEDLIGKLTSLQLQHL
FMILASPRYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLLLEKTK
ELQKLIEADISKRYSGRPVNLMGTSL
Sequence of entity 6 (C), FASTA
>8OHD_6 DDRGK domain-containing protein 1 (chains C)
MVAPVWYLVAAALLVGFILFLTRSRGRAASAGQEPLHNEELAGAGRVAQPGPLEPEEPRA
GGRPRRRRDLGSRLQAQRRAQRVAWAEADENEEEAVILAQEEEGVEKPAETHLSGKIGAK
KLRKLEEKQARKAQREAEEAEREERKRLESQREAEWKKEEERLRLEEEQKEEEERKAREE
QAQREHEEYLKLKEAFVVEEEGVGETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGL
RTQDTINRIQDLLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVSIAELAQASNS
LIAWGRESPAQAPA
Sequence of entity 7 (D), FASTA
>8OHD_7 Ubiquitin-fold modifier 1 (chains D)
MSKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPA
QTAGNVFLKHGSELRIIPRDRVGSC
Sequence of entity 8 (K), FASTA
>8OHD_8 Eukaryotic translation initiation factor 6 (chains K)
MAVRASFENNCEIGCFAKLTNTYCLVAIGGSENFYSVFEGELSDTIPVVHASIAGCRIIG
RMCVGNRHGLLVPNNTTDQELQHIRNSLPDTVQIRRVEERLSALGNVTTCNDYVALVHPD
LDRETEEILADVLKVEVFRQTVADQVLVGSYCVFSNQGGLVHPKTSIEDQDELSSLLQVP
LVAGTVNRGSEVIAAGMVVNDWCAFCGLDTTSTELSVVESVFKLNEAQPSTIATSMRDSL
IDSLT
Sequence of entity 9 (LA), FASTA
>8OHD_9 60S ribosomal protein L8 (chains LA)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 10 (LB), FASTA
>8OHD_10 60S ribosomal protein L3 (chains LB)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 11 (LC), FASTA
>8OHD_11 60S ribosomal protein L4 (chains LC)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDKAAAAAAA
LQAKSDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKPAPEKKPAEKKPTT
EEKKPAA
Sequence of entity 12 (LD), FASTA
>8OHD_12 60S ribosomal protein L5 (chains LD)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMY
KKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 5 |
| MG | Magnesium ion | Mg | 220 |
Primary citation
UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. DaRosa, P.A., Penchev, I., Gumbin, S.C. et al. Nature (2024) 627:445-452. DOI 10.1038/s41586-024-07073-0 · PubMed
Other PDB entries of the same protein (UniProt O94874 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8QFD 2.2 Å, UFL1 E3 ligase bound 60S ribosome
- 8C0D 2.56 Å, UFL1/DDRGK1 bound to UFC1
- 8OJ5 2.9 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution)
- 9GY4 3.0 Å, 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF…
- 8B9X 3.07 Å, Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1
- 8QFC 3.2 Å, UFL1 E3 ligase bound 60S ribosome
- 8OJ0 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native)
- 8OJ8 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)
Browse structure collections
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