8V84: 60S ribosome biogenesis intermediate
60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map). Determined by electron microscopy at 2.7 Å resolution. Released 1 May 2024.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organisms
- Saccharomyces cerevisiae BY4741, Saccharomyces cerevisiae BY4741-AV16
- Chains
- 49
- Atoms
- 121,244
- Mol. weight
- 2794.65 kDa
- Ligands
- ZN, MG, GDP
- Released
- 1 May 2024
Explore 8V84 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8V84 contains 467 α-helices and 419 β-strands across 46 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 3: 21 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 352-358 | 7 | 14 |
| α-helix | 364-370 | 7 | |
| α-helix | 371-375 | 5 | |
| α-helix | 378-381 | 4 | |
| α-helix | 383-392 | 10 | |
| β-strand | 435-438 | 4 | 14 |
| α-helix | 441-455 | 15 | |
| β-strand | 460-461 | 2 | 14 |
| α-helix | 468-480 | 13 | |
| β-strand | 485-488 | 4 | 14 |
| α-helix | 490-494 | 5 | |
| β-strand | 503-506 | 4 | 14 |
| α-helix | 513-520 | 8 | |
| α-helix | 521-523 | 3 | |
| β-strand | 530-536 | 7 | 14 |
| α-helix | 541-551 | 11 | |
| β-strand | 556 | 1 | 14 |
| α-helix | 558-570 | 13 | |
| α-helix | 584-586 | 3 | |
| β-strand | 594-596 | 3 | 14 |
| β-strand | 597 | 1 | 15 |
| α-helix | 600-616 | 17 | |
| α-helix | 619-636 | 18 | |
| α-helix | 639-642 | 4 | |
| α-helix | 643-655 | 13 | |
| β-strand | 660 | 1 | 15 |
| α-helix | 662-664 | 3 | |
| α-helix | 667 | 1 | |
| α-helix | 670-680 | 11 | |
| α-helix | 688-691 | 4 | |
| α-helix | 699-728 | 30 | |
Chain 7: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 106-114 | 9 | |
Chain 8: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 263-264 | 2 | 20 |
| β-strand | 269 | 1 | 24 |
| α-helix | 274 | 1 | |
| β-strand | 275 | 1 | 24 |
| β-strand | 276 | 1 | 25 |
| β-strand | 283 | 1 | 25 |
| α-helix | 297-312 | 16 | |
| α-helix | 316-336 | 21 | |
| α-helix | 344-393 | 50 | |
| α-helix | 401-408 | 8 | |
Chain a: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-22 | 14 | |
| β-strand | 31-37 | 7 | 21 |
| β-strand | 54 | 1 | 22 |
| β-strand | 65-69 | 5 | 23 |
| α-helix | 71-80 | 10 | |
| β-strand | 85-86 | 2 | 23 |
| α-helix | 87-90 | 4 | |
| α-helix | 97-106 | 10 | |
| β-strand | 109-112 | 4 | 23 |
| α-helix | 120-123 | 4 | |
| α-helix | 125-131 | 7 | |
| α-helix | 144-152 | 9 | |
| β-strand | 154 | 1 | 22 |
| β-strand | 164-171 | 8 | 21 |
| α-helix | 176-193 | 18 | |
| β-strand | 205-208 | 4 | 21 |
| α-helix | 212-213 | 2 | |
| β-strand | 214-215 | 2 | 21 |
Chain A: 9 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 33-37 | 5 | 28 |
| β-strand | 38 | 1 | 29 |
| α-helix | 43-55 | 13 | |
| β-strand | 59-61 | 3 | 28 |
| α-helix | 63-64 | 2 | |
| β-strand | 65 | 1 | 29 |
| α-helix | 73-81 | 9 | |
| β-strand | 85-92 | 8 | 28 |
| β-strand | 96-102 | 7 | 28 |
| β-strand | 109-118 | 10 | 28 |
| β-strand | 130 | 1 | 30 |
| β-strand | 134-139 | 6 | 28 |
| α-helix | 141-144 | 4 | |
| α-helix | 147-160 | 14 | |
| α-helix | 162-163 | 2 | |
| β-strand | 173-182 | 10 | 28 |
| β-strand | 185-195 | 11 | 28 |
| β-strand | 210-214 | 5 | 28 |
| β-strand | 218-227 | 10 | 28 |
| β-strand | 235-238 | 4 | 28 |
| α-helix | 245-276 | 32 | |
| α-helix | 280-282 | 3 | |
| α-helix | 286-289 | 4 | |
Chain b: 24 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-10 | 3 | |
| α-helix | 14-28 | 15 | |
| α-helix | 39-67 | 29 | |
| α-helix | 69-70 | 2 | |
| α-helix | 71-73 | 3 | |
| α-helix | 76-86 | 11 | |
| α-helix | 88-115 | 28 | |
| α-helix | 116-118 | 3 | |
| α-helix | 122-141 | 20 | |
| α-helix | 144-157 | 14 | |
| β-strand | 169-174 | 6 | 26 |
| α-helix | 180-187 | 8 | |
| β-strand | 205-211 | 7 | 26 |
| β-strand | 214-220 | 7 | 26 |
| α-helix | 229-231 | 3 | |
| α-helix | 234-244 | 11 | |
| β-strand | 248-254 | 7 | 26 |
| α-helix | 264-274 | 11 | |
| α-helix | 275-278 | 4 | |
| β-strand | 283-287 | 5 | 26 |
| α-helix | 306-309 | 4 | |
| β-strand | 317-319 | 3 | 26 |
| α-helix | 325-340 | 16 | |
| α-helix | 380-384 | 5 | |
| α-helix | 386-388 | 3 | |
| α-helix | 395-397 | 3 | |
| α-helix | 399-406 | 8 | |
| α-helix | 416-419 | 4 | |
| β-strand | 435-436 | 2 | 27 |
| β-strand | 439-440 | 2 | 27 |
| α-helix | 441-444 | 4 | |
| α-helix | 450-466 | 17 | |
Chain B: 14 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-16 | 3 | |
| α-helix | 33-35 | 3 | |
| β-strand | 42-43 | 2 | 32 |
| β-strand | 45-59 | 15 | 33 |
| β-strand | 71-80 | 10 | 33 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-95 | 12 | 34 |
| β-strand | 98-106 | 9 | 34 |
| α-helix | 112-116 | 5 | |
| α-helix | 131-139 | 9 | |
| α-helix | 142-154 | 13 | |
| β-strand | 157-164 | 8 | 34 |
| α-helix | 166-168 | 3 | |
| β-strand | 178-182 | 5 | 34 |
| β-strand | 183-184 | 2 | 32 |
| α-helix | 188-197 | 10 | |
| β-strand | 202-203 | 2 | 34 |
| α-helix | 205-207 | 3 | |
| β-strand | 214-220 | 7 | 33 |
| α-helix | 221-223 | 3 | |
| β-strand | 274-286 | 13 | 33 |
| β-strand | 299 | 1 | 27 |
| α-helix | 307 | 1 | |
| β-strand | 311 | 1 | 35 |
| β-strand | 315 | 1 | 35 |
| β-strand | 321-325 | 5 | 33 |
| β-strand | 335-340 | 6 | 33 |
| α-helix | 348-351 | 4 | |
| α-helix | 353-354 | 2 | |
| β-strand | 356-359 | 4 | 33 |
| α-helix | 373-380 | 8 | |
Chain C: 24 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-9 | 5 | 37 |
| β-strand | 15-21 | 7 | 37 |
| 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 | 38 |
| β-strand | 75-77 | 3 | 38 |
| β-strand | 88 | 1 | 38 |
| α-helix | 98-99 | 2 | |
| α-helix | 115-128 | 14 | |
| α-helix | 132-138 | 7 | |
| β-strand | 150-152 | 3 | 37 |
| α-helix | 154-158 | 5 | |
| α-helix | 162-172 | 11 | |
| α-helix | 175-183 | 9 | |
| β-strand | 186-187 | 2 | 39 |
| α-helix | 188-189 | 2 | |
| α-helix | 191-194 | 4 | |
| β-strand | 199-200 | 2 | 39 |
| β-strand | 206-209 | 4 | 37 |
| α-helix | 215-220 | 6 | |
| β-strand | 226-229 | 4 | 37 |
| β-strand | 232 | 1 | 37 |
| α-helix | 235-238 | 4 | |
| α-helix | 240-242 | 3 | |
| β-strand | 248-251 | 4 | 37 |
| α-helix | 252-262 | 11 | |
| α-helix | 276-279 | 4 | |
| α-helix | 286-290 | 5 | |
| α-helix | 293-296 | 4 | |
| α-helix | 300-301 | 2 | |
| α-helix | 307-309 | 3 | |
| α-helix | 321-327 | 7 | |
| α-helix | 331-337 | 7 | |
| α-helix | 339-341 | 3 | |
38 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 25S ribosomal RNA | 1 | RNA | 3396 | Saccharomyces cerevisiae BY4741 | |
| Saccharomyces cerevisiae 5.8S ribosomal RNA | 2 | RNA | 158 | Saccharomyces cerevisiae BY4741 | |
| ATP-dependent RNA helicase DBP10 | 3 | protein | 995 | Saccharomyces cerevisiae BY4741 | Q12389 (AlphaFold model) |
| ITS2 RNA | 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) |
| Large ribosomal subunit protein uL3 | B | protein | 387 | Saccharomyces cerevisiae BY4741-AV16 | P14126 |
| 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 |
37 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>8V84_1 Saccharomyces cerevisiae 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
>8V84_2 Saccharomyces cerevisiae 5.8S ribosomal RNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 3 (3), FASTA
>8V84_3 ATP-dependent RNA helicase DBP10 (chains 3)
MAGVQKRKRDLEDQDDNGSEEDDIAFDIANEIALNDSESDANDSDSEVEADYGPNDVQDV
IEYSSDEEEGVNNKKKAENKDIKKKKNSKKEIAAFPMLEMSDDENNASGKTQTGDDEDDV
NEYFSTNNLEKTKHKKGSFPSFGLSKIVLNNIKRKGFRQPTPIQRKTIPLILQSRDIVGM
ARTGSGKTAAFILPMVEKLKSHSGKIGARAVILSPSRELAMQTFNVFKDFARGTELRSVL
LTGGDSLEEQFGMMMTNPDVIIATPGRFLHLKVEMNLDLKSVEYVVFDEADRLFEMGFQE
QLNELLASLPTTRQTLLFSATLPNSLVDFVKAGLVNPVLVRLDAETKVSENLEMLFLSSK
NADREANLLYILQEIIKIPLATSEQLQKLQNSNNEADSDSDDENDRQKKRRNFKKEKFRK
QKMPAANELPSEKATILFVPTRHHVEYISQLLRDCGYLISYIYGTLDQHARKRQLYNFRA
GLTSILVVTDVAARGVDIPMLANVINYTLPGSSKIFVHRVGRTARAGNKGWAYSIVAENE
LPYLLDLELFLGKKILLTPMYDSLVDVMKKRWIDEGKPEYQFQPPKLSYTKRLVLGSCPR
LDVEGLGDLYKNLMSSNFDLQLAKKTAMKAEKLYYRTRTSASPESLKRSKEIISSGWDAQ
NAFFGKNEEKEKLDFLAKLQNRRNKETVFEFTRNPDDEMAVFMKRRRKQLAPIQRKATER
RELLEKERMAGLSHSIEDEILKGDDGETGYTVSEDALKEFEDADQLLEAQENENKKKKKP
KSFKDPTFFLSHYAPAGDIQDKQLQITNGFANDAAQAAYDLNSDDKVQVHKQTATVKWDK
KRKKYVNTQGIDNKKYIIGESGQKIAASFRSGRFDDWSKARNLKPLKVGSRETSIPSNLL
EDPSQGPAANGRTVRGKFKHKQMKAPKMPDKHRDNYYSQKKKVEKALQSGISVKGYNNAP
GLRSELKSTEQIRKDRIIAEKKRAKNARPSKKRKF
Sequence of entity 4 (6), FASTA
>8V84_4 ITS2 RNA (chains 6)
CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCU
GGCCUUUUCAUUGGAUGUUUUUUUUCCAAAGAGAGGUUUCUCUGCGUGCUUGAGGUAUAA
UGCAAGUACGGUCGUUUUAGGUUUUACCAACUGCGGCUAAUCUUUUUUUAUACUGAGCGU
AUUGGAACGUUAUCGAUAAGAAGAGAGCGUCUAGGCGAACAAUGUUCUUAAA
Sequence of entity 5 (7), FASTA
>8V84_5 60S ribosomal subunit assembly/export protein LOC1 (chains 7)
MAPKKPSKRQNLRREVAPEVFQDSQARNQLANVPHLTEKSAQRKPSKTKVKKEQSLARLY
GAKKDKKGKYSEKDLNIPTLNRAIVPGVKIRRGKKGKKFIADNDTLTLNRLITTIGDKYD
DIAESKLEKARRLEEIRELKRKEIERKEALKQDKLEEKKDEIKKKSSVARTIRRKNKRDM
LKSEAKASESKTEGRKVKKVSFAQ
Sequence of entity 6 (8), FASTA
>8V84_6 Ribosomal RNA-processing protein 14 (chains 8)
MSNSLEERLRANSSAFDGLLALIPAKYYYDEKSQEQWKAKKKTKEQSKNDKLKKLDPEQR
DDETSSTLEVMKKKEKDAKPVVLPGEKFKHMKMQKQKEATSKVEGDSDLNVEVNDPMIIA
PDEDEEEEEDIKVIFDDEGNEIPLESKKDTTEPDRSVEKKSITEEEKLQRKKNLEALRSK
LQAKISDMKSKRKAPGSREAILAQRKRKEELKKRKRLESEQEQDQDEIASDSDMEDIDSD
LENNSKKRFKKGKKDSEINADGVMFQNIIFDDGARATSDLQRLRKAGRTKGPAKNDVKSH
LKLLEAKKNKMEAKDELEQIKQKEKEKWQKAMLQAEGIKIRDDEKLLRKAIKRKEAQKRK
SAIEWSERKRVVEDTISERQKRREENLRIRKDNKGKKRNKQEKMKRKYVGSAVPKKRAGF
EGRLKTGKKKGGPK
Sequence of entity 7 (A), FASTA
>8V84_7 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
Sequence of entity 8 (B), FASTA
>8V84_8 Large ribosomal subunit protein uL3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 9 (C), FASTA
>8V84_9 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 10 (D), FASTA
>8V84_10 ATP-dependent RNA helicase HAS1 (chains D)
MATPSNKRSRDSESTEEPVVDEKSTSKQNNAAPEGEQTTCVEKFEELKLSQPTLKAIEKM
GFTTMTSVQARTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIELLHSLKFKPRNGTGIIVI
TPTRELALQIFGVARELMEFHSQTFGIVIGGANRRQEAEKLMKGVNMLIATPGRLLDHLQ
NTKGFVFKNLKALIIDEADRILEIGFEDEMRQIIKILPNEDRQSMLFSATQTTKVEDLAR
ISLRPGPLFINVVPETDNSTADGLEQGYVVCDSDKRFLLLFSFLKRNQKKKIIVFLSSCN
SVKYYAELLNYIDLPVLELHGKQKQQKRTNTFFEFCNAERGILICTDVAARGLDIPAVDW
IIQFDPPDDPRDYIHRVGRTARGTKGKGKSLMFLTPNELGFLRYLKASKVPLNEYEFPEN
KIANVQSQLEKLIKSNYYLHQTAKDGYRSYLQAYASHSLKTVYQIDKLDLAKVAKSYGFP
VPPKVNITIGASGKTPNTKRRKTHK
Sequence of entity 11 (E), FASTA
>8V84_11 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 12 (F), FASTA
>8V84_12 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| MG | Magnesium ion | Mg | 1 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
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 Q12389 (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)
- 8V85 2.9 Å, 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Low-pass filtered…
Browse structure collections
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