8V83: 60S ribosome biogenesis intermediate
60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map). Determined by electron microscopy at 2.53 Å resolution. Released 1 May 2024.
- Method
- Electron microscopy
- Resolution
- 2.53 Å
- Organism
- Saccharomyces cerevisiae BY4741
- Chains
- 48
- Atoms
- 119,224
- Mol. weight
- 2681.05 kDa
- Ligands
- ZN
- Released
- 1 May 2024
Explore 8V83 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8V83 contains 463 α-helices and 406 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 7: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 106-114 | 9 | |
Chain 8: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 263-265 | 3 | 11 |
| β-strand | 268 | 1 | 15 |
| β-strand | 269 | 1 | 16 |
| β-strand | 275 | 1 | 16 |
| β-strand | 276 | 1 | 17 |
| β-strand | 283 | 1 | 17 |
| α-helix | 297-313 | 17 | |
| α-helix | 316-336 | 21 | |
| α-helix | 344-393 | 50 | |
| α-helix | 398-400 | 3 | |
| α-helix | 401-408 | 8 | |
Chain a: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-22 | 14 | |
| β-strand | 32-37 | 6 | 12 |
| β-strand | 53 | 1 | 13 |
| β-strand | 65-69 | 5 | 14 |
| α-helix | 71-80 | 10 | |
| β-strand | 85-86 | 2 | 14 |
| α-helix | 87-91 | 5 | |
| α-helix | 97-106 | 10 | |
| β-strand | 109-112 | 4 | 14 |
| α-helix | 120-124 | 5 | |
| α-helix | 127-131 | 5 | |
| α-helix | 144-152 | 9 | |
| β-strand | 155 | 1 | 13 |
| β-strand | 164-170 | 7 | 12 |
| α-helix | 176-193 | 18 | |
| β-strand | 205-208 | 4 | 12 |
| α-helix | 211-213 | 3 | |
| β-strand | 214-215 | 2 | 12 |
Chain A: 10 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 33-37 | 5 | 20 |
| β-strand | 38 | 1 | 21 |
| α-helix | 43-55 | 13 | |
| β-strand | 59-61 | 3 | 20 |
| α-helix | 63-64 | 2 | |
| β-strand | 65 | 1 | 21 |
| α-helix | 73-81 | 9 | |
| β-strand | 85-92 | 8 | 20 |
| β-strand | 96-102 | 7 | 20 |
| β-strand | 109-118 | 10 | 20 |
| β-strand | 130 | 1 | 22 |
| α-helix | 133 | 1 | |
| β-strand | 134-140 | 7 | 20 |
| α-helix | 141-144 | 4 | |
| α-helix | 147-160 | 14 | |
| α-helix | 162-163 | 2 | |
| β-strand | 173-182 | 10 | 20 |
| β-strand | 185-195 | 11 | 20 |
| β-strand | 210-214 | 5 | 20 |
| β-strand | 218-227 | 10 | 20 |
| β-strand | 235-238 | 4 | 20 |
| α-helix | 245-276 | 32 | |
| α-helix | 280-282 | 3 | |
| α-helix | 286-289 | 4 | |
Chain b: 22 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-10 | 3 | |
| α-helix | 14-28 | 15 | |
| α-helix | 39-66 | 28 | |
| α-helix | 71-73 | 3 | |
| α-helix | 76-85 | 10 | |
| α-helix | 88-117 | 30 | |
| α-helix | 122-142 | 21 | |
| α-helix | 144-157 | 14 | |
| β-strand | 169-174 | 6 | 18 |
| α-helix | 180-187 | 8 | |
| β-strand | 205-211 | 7 | 18 |
| β-strand | 214-220 | 7 | 18 |
| α-helix | 221-223 | 3 | |
| α-helix | 234-245 | 12 | |
| β-strand | 248-253 | 6 | 18 |
| α-helix | 264-274 | 11 | |
| α-helix | 275-278 | 4 | |
| β-strand | 283-286 | 4 | 18 |
| α-helix | 306-311 | 6 | |
| β-strand | 315-318 | 4 | 18 |
| α-helix | 325-340 | 16 | |
| α-helix | 380-383 | 4 | |
| α-helix | 386-388 | 3 | |
| α-helix | 396-397 | 2 | |
| α-helix | 399-406 | 8 | |
| α-helix | 416-419 | 4 | |
| β-strand | 435-436 | 2 | 19 |
| β-strand | 439-440 | 2 | 19 |
| α-helix | 441-444 | 4 | |
| α-helix | 449-466 | 18 | |
Chain B: 13 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-35 | 3 | |
| β-strand | 42-43 | 2 | 24 |
| β-strand | 45-60 | 16 | 25 |
| β-strand | 70-80 | 11 | 25 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-95 | 12 | 26 |
| β-strand | 98-106 | 9 | 26 |
| α-helix | 112-115 | 4 | |
| α-helix | 116-118 | 3 | |
| α-helix | 131-139 | 9 | |
| α-helix | 142-154 | 13 | |
| β-strand | 157-163 | 7 | 26 |
| α-helix | 176-177 | 2 | |
| β-strand | 178-182 | 5 | 26 |
| β-strand | 183-184 | 2 | 24 |
| α-helix | 188-198 | 11 | |
| β-strand | 202-203 | 2 | 26 |
| α-helix | 205-207 | 3 | |
| β-strand | 214-220 | 7 | 25 |
| α-helix | 221-223 | 3 | |
| β-strand | 274-286 | 13 | 25 |
| β-strand | 299 | 1 | 19 |
| α-helix | 307 | 1 | |
| β-strand | 311 | 1 | 27 |
| β-strand | 315 | 1 | 27 |
| β-strand | 321-325 | 5 | 25 |
| β-strand | 335-340 | 6 | 25 |
| α-helix | 348-351 | 4 | |
| β-strand | 356-359 | 4 | 25 |
| α-helix | 373-380 | 8 | |
Chain C: 24 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-9 | 5 | 29 |
| β-strand | 15-21 | 7 | 29 |
| α-helix | 22-23 | 2 | |
| α-helix | 24-27 | 4 | |
| α-helix | 32-42 | 11 | |
| α-helix | 47-49 | 3 | |
| β-strand | 62-64 | 3 | 30 |
| β-strand | 75-77 | 3 | 30 |
| β-strand | 88 | 1 | 30 |
| α-helix | 98-99 | 2 | |
| α-helix | 115-129 | 15 | |
| α-helix | 132-138 | 7 | |
| β-strand | 150-152 | 3 | 29 |
| α-helix | 154-158 | 5 | |
| α-helix | 162-171 | 10 | |
| α-helix | 175-183 | 9 | |
| β-strand | 186-187 | 2 | 31 |
| α-helix | 188 | 1 | |
| α-helix | 191-194 | 4 | |
| β-strand | 199-200 | 2 | 31 |
| β-strand | 206-209 | 4 | 29 |
| α-helix | 215-219 | 5 | |
| β-strand | 226-229 | 4 | 29 |
| α-helix | 235-238 | 4 | |
| α-helix | 240-242 | 3 | |
| β-strand | 248-251 | 4 | 29 |
| α-helix | 252-262 | 11 | |
| β-strand | 267 | 1 | 32 |
| α-helix | 276-279 | 4 | |
| α-helix | 286-290 | 5 | |
| α-helix | 293-296 | 4 | |
| α-helix | 300-302 | 3 | |
| α-helix | 307-309 | 3 | |
| α-helix | 321-327 | 7 | |
| α-helix | 330-337 | 8 | |
| α-helix | 339-341 | 3 | |
Chain D: 24 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 43 | 1 | 34 |
| α-helix | 51-60 | 10 | |
| β-strand | 64 | 1 | 34 |
| α-helix | 67-78 | 12 | |
| β-strand | 82-85 | 4 | 35 |
| α-helix | 92-107 | 16 | |
| α-helix | 111-113 | 3 | |
| β-strand | 117-120 | 4 | 35 |
| α-helix | 124-137 | 14 | |
| α-helix | 138-140 | 3 | |
| β-strand | 145-148 | 4 | 35 |
| α-helix | 154-163 | 10 | |
| β-strand | 167-170 | 4 | 35 |
| α-helix | 172-181 | 10 | |
| β-strand | 192-196 | 5 | 35 |
| α-helix | 198-204 | 7 | |
| α-helix | 207-216 | 10 | |
| β-strand | 223-228 | 6 | 35 |
| α-helix | 233-242 | 10 | |
| α-helix | 244 | 1 | |
| β-strand | 248-251 | 4 | 35 |
| β-strand | 267-270 | 4 | 36 |
| α-helix | 273-286 | 14 | |
| β-strand | 291-296 | 6 | 36 |
| α-helix | 299-311 | 13 | |
| β-strand | 317-319 | 3 | 36 |
| α-helix | 325-337 | 13 | |
| β-strand | 341-346 | 6 | 36 |
| α-helix | 347-350 | 4 | |
| β-strand | 360-363 | 4 | 36 |
| α-helix | 366-367 | 2 | |
| α-helix | 370-373 | 4 | |
| β-strand | 389-394 | 6 | 36 |
| α-helix | 396-398 | 3 | |
| α-helix | 401-407 | 7 | |
| β-strand | 414 | 1 | 36 |
| α-helix | 426-435 | 10 | |
| α-helix | 437-456 | 20 | |
| α-helix | 470-477 | 8 | |
| α-helix | 482-484 | 3 | |
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 25S ribosomal RNA | 1 | RNA | 3396 | Saccharomyces cerevisiae BY4741 | |
| Saccharomyces cerevisiae S288C 5.8S ribosomal RNA | 2 | RNA | 158 | Saccharomyces cerevisiae BY4741 | |
| Saccharomyces cerevisiae ITS-2 | 6 | RNA | 232 | Saccharomyces cerevisiae BY4741 | |
| 60S ribosomal subunit assembly/export protein LOC1 | 7 | protein | 204 | Saccharomyces cerevisiae BY4741 | P43586 (AlphaFold model) |
| Ribosomal RNA-processing protein 14 | 8 | protein | 434 | Saccharomyces cerevisiae BY4741 | P36080 (AlphaFold model) |
| Ribosome biogenesis protein BRX1 | A | protein | 291 | Saccharomyces cerevisiae BY4741 | Q08235 (AlphaFold model) |
| 60S ribosomal protein L3 | B | protein | 387 | Saccharomyces cerevisiae BY4741 | P14126 (AlphaFold model) |
| 60S ribosomal protein L4-A | C | protein | 362 | Saccharomyces cerevisiae BY4741 | P10664 |
| ATP-dependent RNA helicase HAS1 | D | protein | 505 | Saccharomyces cerevisiae BY4741 | Q03532 |
| 60S ribosomal protein L6-A | E | protein | 176 | Saccharomyces cerevisiae BY4741 | Q02326 |
| 60S ribosomal protein L7-A | F | protein | 244 | Saccharomyces cerevisiae BY4741 | P05737 |
| Large ribosomal subunit protein eL8A | G | protein | 256 | Saccharomyces cerevisiae BY4741 | P17076 |
36 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>8V83_1 Saccharomyces cerevisiae S288C 25S ribosomal RNA (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 (2), FASTA
>8V83_2 Saccharomyces cerevisiae S288C 5.8S ribosomal RNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 3 (6), FASTA
>8V83_3 Saccharomyces cerevisiae ITS-2 (chains 6)
CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCU
GGCCUUUUCAUUGGAUGUUUUUUUUCCAAAGAGAGGUUUCUCUGCGUGCUUGAGGUAUAA
UGCAAGUACGGUCGUUUUAGGUUUUACCAACUGCGGCUAAUCUUUUUUUAUACUGAGCGU
AUUGGAACGUUAUCGAUAAGAAGAGAGCGUCUAGGCGAACAAUGUUCUUAAA
Sequence of entity 4 (7), FASTA
>8V83_4 60S ribosomal subunit assembly/export protein LOC1 (chains 7)
MAPKKPSKRQNLRREVAPEVFQDSQARNQLANVPHLTEKSAQRKPSKTKVKKEQSLARLY
GAKKDKKGKYSEKDLNIPTLNRAIVPGVKIRRGKKGKKFIADNDTLTLNRLITTIGDKYD
DIAESKLEKARRLEEIRELKRKEIERKEALKQDKLEEKKDEIKKKSSVARTIRRKNKRDM
LKSEAKASESKTEGRKVKKVSFAQ
Sequence of entity 5 (8), FASTA
>8V83_5 Ribosomal RNA-processing protein 14 (chains 8)
MSNSLEERLRANSSAFDGLLALIPAKYYYDEKSQEQWKAKKKTKEQSKNDKLKKLDPEQR
DDETSSTLEVMKKKEKDAKPVVLPGEKFKHMKMQKQKEATSKVEGDSDLNVEVNDPMIIA
PDEDEEEEEDIKVIFDDEGNEIPLESKKDTTEPDRSVEKKSITEEEKLQRKKNLEALRSK
LQAKISDMKSKRKAPGSREAILAQRKRKEELKKRKRLESEQEQDQDEIASDSDMEDIDSD
LENNSKKRFKKGKKDSEINADGVMFQNIIFDDGARATSDLQRLRKAGRTKGPAKNDVKSH
LKLLEAKKNKMEAKDELEQIKQKEKEKWQKAMLQAEGIKIRDDEKLLRKAIKRKEAQKRK
SAIEWSERKRVVEDTISERQKRREENLRIRKDNKGKKRNKQEKMKRKYVGSAVPKKRAGF
EGRLKTGKKKGGPK
Sequence of entity 6 (A), FASTA
>8V83_6 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
Sequence of entity 7 (B), FASTA
>8V83_7 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 8 (C), FASTA
>8V83_8 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 9 (D), FASTA
>8V83_9 ATP-dependent RNA helicase HAS1 (chains D)
MATPSNKRSRDSESTEEPVVDEKSTSKQNNAAPEGEQTTCVEKFEELKLSQPTLKAIEKM
GFTTMTSVQARTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIELLHSLKFKPRNGTGIIVI
TPTRELALQIFGVARELMEFHSQTFGIVIGGANRRQEAEKLMKGVNMLIATPGRLLDHLQ
NTKGFVFKNLKALIIDEADRILEIGFEDEMRQIIKILPNEDRQSMLFSATQTTKVEDLAR
ISLRPGPLFINVVPETDNSTADGLEQGYVVCDSDKRFLLLFSFLKRNQKKKIIVFLSSCN
SVKYYAELLNYIDLPVLELHGKQKQQKRTNTFFEFCNAERGILICTDVAARGLDIPAVDW
IIQFDPPDDPRDYIHRVGRTARGTKGKGKSLMFLTPNELGFLRYLKASKVPLNEYEFPEN
KIANVQSQLEKLIKSNYYLHQTAKDGYRSYLQAYASHSLKTVYQIDKLDLAKVAKSYGFP
VPPKVNITIGASGKTPNTKRRKTHK
Sequence of entity 10 (E), FASTA
>8V83_10 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 11 (F), FASTA
>8V83_11 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Sequence of entity 12 (G), FASTA
>8V83_12 Large ribosomal subunit protein eL8A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis. Cruz, V.E., Weirich, C.S., Peddada, N. et al. Nat Commun (2024) 15:3296-3296. DOI 10.1038/s41467-024-47616-7 · PubMed
Other PDB entries of the same protein (UniProt P43586 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8V87 2.66 Å, 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
- 8V84 2.7 Å, 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
- 7NAC 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
- 7R7A 3.04 Å, State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
- 7R6K 3.17 Å, State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region
- 7R7C 3.71 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model
Browse structure collections
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