8I9X: Brix domain-containing protein
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-1. Determined by electron microscopy at 2.8 Å resolution. Released 17 May 2023.
- Method
- Electron microscopy
- Resolution
- 2.8 Å
- Organism
- Chaetomium thermophilum
- Chains
- 60
- Atoms
- 162,633
- Mol. weight
- 3495.68 kDa
- Ligands
- GTP, ZN
- Released
- 17 May 2023
Explore 8I9X in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8I9X contains 634 α-helices and 520 β-strands across 58 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 CA: 8 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-41 | 6 | 10 |
| α-helix | 46-58 | 13 | |
| β-strand | 62-68 | 7 | 10 |
| α-helix | 74-76 | 3 | |
| α-helix | 77-83 | 7 | |
| β-strand | 88-95 | 8 | 10 |
| β-strand | 99-106 | 8 | 10 |
| β-strand | 111-121 | 11 | 10 |
| β-strand | 133 | 1 | 11 |
| β-strand | 136 | 1 | 12 |
| α-helix | 137-138 | 2 | |
| β-strand | 139-142 | 4 | 10 |
| α-helix | 144-147 | 4 | |
| α-helix | 150-162 | 13 | |
| β-strand | 173 | 1 | 12 |
| β-strand | 178-184 | 7 | 10 |
| β-strand | 189-199 | 11 | 10 |
| α-helix | 200-202 | 3 | |
| β-strand | 228-233 | 6 | 10 |
| β-strand | 237-247 | 11 | 10 |
| β-strand | 254-257 | 4 | 10 |
| α-helix | 264-294 | 31 | |
Chain Cb: 37 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-22 | 6 | |
| α-helix | 99-108 | 10 | |
| α-helix | 115-125 | 11 | |
| β-strand | 130-133 | 4 | 1 |
| α-helix | 140-152 | 13 | |
| β-strand | 158 | 1 | 2 |
| β-strand | 163-166 | 4 | 1 |
| α-helix | 170-183 | 14 | |
| β-strand | 185 | 1 | 3 |
| β-strand | 187 | 1 | 3 |
| β-strand | 191-194 | 4 | 1 |
| α-helix | 200-209 | 10 | |
| β-strand | 213-216 | 4 | 1 |
| α-helix | 218-228 | 11 | |
| α-helix | 232-234 | 3 | |
| β-strand | 237-241 | 5 | 1 |
| α-helix | 243-249 | 7 | |
| α-helix | 252-261 | 10 | |
| β-strand | 267-272 | 6 | 1 |
| α-helix | 277-286 | 10 | |
| α-helix | 290 | 1 | |
| β-strand | 291-294 | 4 | 1 |
| β-strand | 305-311 | 7 | 4 |
| α-helix | 314-316 | 3 | |
| α-helix | 317-323 | 7 | |
| α-helix | 324-328 | 5 | |
| α-helix | 331-333 | 3 | |
| β-strand | 369-372 | 4 | 4 |
| α-helix | 376-389 | 14 | |
| β-strand | 393-396 | 4 | 4 |
| α-helix | 402-414 | 13 | |
| β-strand | 419-422 | 4 | 4 |
| α-helix | 425-429 | 5 | |
| β-strand | 437-440 | 4 | 4 |
| α-helix | 447-455 | 9 | |
| β-strand | 464-470 | 7 | 4 |
| α-helix | 475-485 | 11 | |
| β-strand | 489-491 | 3 | 4 |
| β-strand | 504-507 | 4 | 4 |
| β-strand | 508 | 1 | 5 |
| α-helix | 511-527 | 17 | |
| α-helix | 529-548 | 20 | |
| α-helix | 550-551 | 2 | |
| α-helix | 554-565 | 12 | |
| α-helix | 567-570 | 4 | |
| β-strand | 572 | 1 | 5 |
| α-helix | 573 | 1 | |
| α-helix | 574-576 | 3 | |
| α-helix | 578-595 | 18 | |
| α-helix | 616-628 | 13 | |
| α-helix | 715-717 | 3 | |
| β-strand | 795-797 | 3 | 6 |
| β-strand | 803-805 | 3 | 6 |
| α-helix | 812-820 | 9 | |
| α-helix | 824-827 | 4 | |
| β-strand | 831 | 1 | 2 |
| α-helix | 832 | 1 | |
| α-helix | 834-839 | 6 | |
| α-helix | 855-859 | 5 | |
| α-helix | 866-879 | 14 | |
Chain CB: 14 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-39 | 20 | |
| α-helix | 41-42 | 2 | |
| β-strand | 47 | 1 | 16 |
| α-helix | 53-59 | 7 | |
| β-strand | 61-68 | 8 | 17 |
| β-strand | 81-83 | 3 | 18 |
| β-strand | 97-101 | 5 | 19 |
| α-helix | 105-113 | 9 | |
| α-helix | 118-123 | 6 | |
| β-strand | 124-129 | 6 | 19 |
| α-helix | 130-136 | 7 | |
| α-helix | 140-149 | 10 | |
| β-strand | 152-156 | 5 | 19 |
| α-helix | 157-160 | 4 | |
| α-helix | 163-167 | 5 | |
| α-helix | 169-172 | 4 | |
| α-helix | 178-179 | 2 | |
| β-strand | 180-182 | 3 | 19 |
| α-helix | 217-229 | 13 | |
| β-strand | 231-233 | 3 | 18 |
| β-strand | 240-247 | 8 | 17 |
| α-helix | 252-269 | 18 | |
| α-helix | 274-276 | 3 | |
| β-strand | 278-284 | 7 | 17 |
| β-strand | 290-291 | 2 | 17 |
Chain CC: 31 helices, 39 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 123-125 | 3 | |
| β-strand | 137-141 | 5 | 23 |
| β-strand | 147-151 | 5 | 23 |
| α-helix | 152-154 | 3 | |
| β-strand | 185-188 | 4 | 24 |
| α-helix | 193 | 1 | |
| β-strand | 194-196 | 3 | 24 |
| α-helix | 197 | 1 | |
| α-helix | 203-211 | 9 | |
| β-strand | 217-221 | 5 | 25 |
| β-strand | 228-230 | 3 | 25 |
| α-helix | 233-244 | 12 | |
| α-helix | 256-259 | 4 | |
| α-helix | 266-267 | 2 | |
| α-helix | 274-277 | 4 | |
| α-helix | 278-280 | 3 | |
| α-helix | 283-284 | 2 | |
| α-helix | 285-300 | 16 | |
| α-helix | 304-306 | 3 | |
| α-helix | 309-315 | 7 | |
| α-helix | 334-336 | 3 | |
| α-helix | 341-348 | 8 | |
| β-strand | 353 | 1 | 26 |
| α-helix | 358-360 | 3 | |
| α-helix | 361-363 | 3 | |
| α-helix | 364-372 | 9 | |
| α-helix | 374 | 1 | |
| α-helix | 394-396 | 3 | |
| α-helix | 399-412 | 14 | |
| β-strand | 415-421 | 7 | 27 |
| α-helix | 425-427 | 3 | |
| α-helix | 430-431 | 2 | |
| α-helix | 436-438 | 3 | |
| β-strand | 445-449 | 5 | 28 |
| β-strand | 456-461 | 6 | 29 |
| β-strand | 467-472 | 6 | 29 |
| β-strand | 476-481 | 6 | 29 |
| β-strand | 487-492 | 6 | 29 |
| α-helix | 498 | 1 | |
| β-strand | 499-504 | 6 | 30 |
| β-strand | 513-517 | 5 | 30 |
| β-strand | 520-524 | 5 | 30 |
| α-helix | 533-543 | 11 | |
| β-strand | 568-570 | 3 | 30 |
| α-helix | 574-579 | 6 | |
| β-strand | 581-586 | 6 | 30 |
| β-strand | 593-596 | 4 | 31 |
| β-strand | 602-606 | 5 | 31 |
| α-helix | 611-613 | 3 | |
| β-strand | 615-619 | 5 | 31 |
| β-strand | 624-626 | 3 | 31 |
| β-strand | 636-641 | 6 | 32 |
| β-strand | 647-652 | 6 | 32 |
| β-strand | 656-660 | 5 | 32 |
| β-strand | 665-670 | 6 | 32 |
| β-strand | 677-682 | 6 | 33 |
| β-strand | 688-693 | 6 | 33 |
| β-strand | 697-702 | 6 | 33 |
| β-strand | 711-713 | 3 | 33 |
| β-strand | 720-725 | 6 | 34 |
| β-strand | 732-737 | 6 | 34 |
| β-strand | 741-748 | 8 | 34 |
| α-helix | 756-757 | 2 | |
| β-strand | 758-765 | 8 | 34 |
| α-helix | 768-770 | 3 | |
| β-strand | 771 | 1 | 35 |
| β-strand | 774 | 1 | 35 |
| β-strand | 776-781 | 6 | 28 |
| β-strand | 788-792 | 5 | 28 |
| β-strand | 796-800 | 5 | 28 |
Chain CD: 9 helices, 36 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 14-20 | 7 | 38 |
| β-strand | 34-38 | 5 | 38 |
| α-helix | 43-50 | 8 | |
| β-strand | 63-67 | 5 | 38 |
| β-strand | 70-71 | 2 | 38 |
| α-helix | 76-82 | 7 | |
| α-helix | 90 | 1 | |
| β-strand | 91-97 | 7 | 38 |
| α-helix | 98-102 | 5 | |
| β-strand | 103-106 | 4 | 39 |
| β-strand | 114-120 | 7 | 40 |
| α-helix | 125-131 | 7 | |
| β-strand | 145-150 | 6 | 40 |
| β-strand | 154-159 | 6 | 40 |
| β-strand | 164-167 | 4 | 40 |
| α-helix | 168-170 | 3 | |
| α-helix | 171-173 | 3 | |
| β-strand | 180-185 | 6 | 41 |
| β-strand | 190-195 | 6 | 41 |
| β-strand | 200-209 | 10 | 41 |
| β-strand | 212-221 | 10 | 41 |
| β-strand | 228-234 | 7 | 42 |
| β-strand | 239-244 | 6 | 42 |
| β-strand | 248-253 | 6 | 42 |
| β-strand | 285-287 | 3 | 41 |
| β-strand | 291-293 | 3 | 42 |
| β-strand | 300-305 | 6 | 43 |
| β-strand | 312-317 | 6 | 43 |
| β-strand | 321-326 | 6 | 43 |
| β-strand | 331-337 | 7 | 43 |
| β-strand | 342-348 | 7 | 44 |
| β-strand | 357-362 | 6 | 44 |
| β-strand | 366-370 | 5 | 44 |
| β-strand | 382-384 | 3 | 44 |
| β-strand | 391-396 | 6 | 45 |
| β-strand | 403-408 | 6 | 45 |
| β-strand | 412-417 | 6 | 45 |
| β-strand | 422-423 | 2 | 44 |
| β-strand | 433-435 | 3 | 44 |
| β-strand | 439-441 | 3 | 45 |
| α-helix | 444-449 | 6 | |
| α-helix | 454-455 | 2 | |
| β-strand | 463-468 | 6 | 39 |
| β-strand | 473-477 | 5 | 39 |
| β-strand | 482-486 | 5 | 39 |
Chain CE: 28 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 112 | 1 | 52 |
| α-helix | 120-129 | 10 | |
| β-strand | 133 | 1 | 52 |
| α-helix | 134-135 | 2 | |
| α-helix | 136-147 | 12 | |
| β-strand | 151-154 | 4 | 53 |
| α-helix | 161-176 | 16 | |
| β-strand | 186-189 | 4 | 53 |
| α-helix | 193-206 | 14 | |
| β-strand | 214-217 | 4 | 53 |
| α-helix | 223-232 | 10 | |
| β-strand | 236-239 | 4 | 53 |
| α-helix | 241-250 | 10 | |
| β-strand | 260-264 | 5 | 53 |
| α-helix | 266-272 | 7 | |
| α-helix | 275-284 | 10 | |
| β-strand | 291-296 | 6 | 53 |
| α-helix | 301-310 | 10 | |
| α-helix | 312 | 1 | |
| α-helix | 315 | 1 | |
| β-strand | 316-319 | 4 | 53 |
| α-helix | 325-328 | 4 | |
| β-strand | 334-338 | 5 | 54 |
| α-helix | 344-354 | 11 | |
| β-strand | 359-364 | 6 | 54 |
| α-helix | 367-379 | 13 | |
| β-strand | 385-387 | 3 | 54 |
| α-helix | 393-405 | 13 | |
| β-strand | 409-414 | 6 | 54 |
| α-helix | 415-420 | 6 | |
| β-strand | 428-431 | 4 | 54 |
| α-helix | 438-440 | 3 | |
| α-helix | 441-445 | 5 | |
| α-helix | 446-449 | 4 | |
| β-strand | 457-462 | 6 | 54 |
| α-helix | 464-466 | 3 | |
| α-helix | 468-475 | 8 | |
| β-strand | 480-482 | 3 | 54 |
| β-strand | 483 | 1 | 16 |
| α-helix | 494-503 | 10 | |
| α-helix | 505-523 | 19 | |
| α-helix | 533-535 | 3 | |
| α-helix | 538-545 | 8 | |
| α-helix | 550-552 | 3 | |
| α-helix | 575-578 | 4 | |
Chain CF: 15 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-33 | 14 | |
| α-helix | 34-36 | 3 | |
| β-strand | 39-44 | 6 | 56 |
| α-helix | 53-59 | 7 | |
| β-strand | 64-66 | 3 | 56 |
| α-helix | 70-77 | 8 | |
| α-helix | 89-92 | 4 | |
| β-strand | 100-105 | 6 | 56 |
| α-helix | 109-118 | 10 | |
| β-strand | 121-123 | 3 | 57 |
| α-helix | 129 | 1 | |
| β-strand | 130 | 1 | 58 |
| α-helix | 131 | 1 | |
| β-strand | 135-137 | 3 | 59 |
| α-helix | 138 | 1 | |
| β-strand | 140-141 | 2 | 60 |
| β-strand | 143 | 1 | 61 |
| α-helix | 151-153 | 3 | |
| β-strand | 156 | 1 | 61 |
| α-helix | 157-158 | 2 | |
| α-helix | 162-168 | 7 | |
| β-strand | 173-175 | 3 | 60 |
| β-strand | 178-181 | 4 | 60 |
| β-strand | 192-195 | 4 | 59 |
| β-strand | 200 | 1 | 58 |
| α-helix | 201-202 | 2 | |
| α-helix | 203-211 | 9 | |
| β-strand | 217-219 | 3 | 57 |
| β-strand | 222-228 | 7 | 56 |
| β-strand | 233-236 | 4 | 56 |
| α-helix | 239-241 | 3 | |
Chain CG: 8 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 70 |
| β-strand | 5 | 1 | 71 |
| α-helix | 6-19 | 14 | |
| β-strand | 20 | 1 | 72 |
| α-helix | 24-27 | 4 | |
| β-strand | 36-41 | 6 | 70 |
| β-strand | 44-49 | 6 | 70 |
| α-helix | 50-56 | 7 | |
| α-helix | 61-63 | 3 | |
| β-strand | 64-67 | 4 | 73 |
| β-strand | 69-74 | 6 | 70 |
| β-strand | 80-82 | 3 | 70 |
| α-helix | 87-92 | 6 | |
| β-strand | 94 | 1 | 72 |
| β-strand | 96-100 | 5 | 74 |
| α-helix | 102-110 | 9 | |
| β-strand | 114-115 | 2 | 74 |
| β-strand | 119-121 | 3 | 74 |
| β-strand | 132-135 | 4 | 74 |
| β-strand | 141-147 | 7 | 74 |
| α-helix | 151-155 | 5 | |
| β-strand | 162-169 | 8 | 74 |
| α-helix | 170-173 | 4 | |
50 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 |
|---|
| RNA (3341-mer) | C1 | RNA | 3341 | Chaetomium thermophilum | |
| RNA (319-mer) | C2 | RNA | 319 | Chaetomium thermophilum | |
| Brix domain-containing protein | CA | protein | 316 | Chaetomium thermophilum | G0RXZ3 (AlphaFold model) |
| Ribosome biogenesis protein C8F11.04 | CB | protein | 391 | Chaetomium thermophilum | G0S7X0 (AlphaFold model) |
| Ribosome biogenesis protein ERB1 | CC | protein | 801 | Chaetomium thermophilum | G0SCK6 (AlphaFold model) |
| Ribosome biogenesis protein YTM1 | CD | protein | 495 | Chaetomium thermophilum | G0SFB5 (AlphaFold model) |
| RNA helicase | CE | protein | 598 | Chaetomium thermophilum | G0RYU9 |
| Ribosome assembly factor mrt4 | CF | protein | 270 | Chaetomium thermophilum | G0S616 |
| 60S ribosome subunit biogenesis protein NIP7 | CG | protein | 184 | Chaetomium thermophilum | G0S435 |
| Nucleolar GTP-binding protein 1 | CH | protein | 661 | Chaetomium thermophilum | G0S8F1 |
| Putative RNA-binding protein | CI | protein | 414 | Chaetomium thermophilum | G0S1H0 |
| Pescadillo homolog | CJ | protein | 679 | Chaetomium thermophilum | G0SHX6 |
47 more molecules are not listed.
Sequence of entity 1 (C1), FASTA
>8I9X_1 RNA (3341-MER) (chains C1)
GGUUGACCUCGGAUCAGGUAGGAGGACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACAGGGAUUGCCCUAGUAACGGCGAGUGAAGCGGCAACAGCUCAAAUUUG
AAAGCUGGCUUCGGCCCGCGUUGUAAUUUGGAGAGGAUGCUUUGGGCGAGGCUCCUUCUG
AGUUCCCUGGAACGGGACGCCACAGAGGGUGAGAGCCCCGUAUAGUUGGAAGCCAAGCCU
GUGUAAAGCUCCUUCGACGAGUCGAGUAGUUUGGGAAUGCUGCUCAAAAUGGGAGGUAAA
UUUCUUCUAAAGCUAAAUACCGGCCAGAGACCGAUAGCGCACAAGUAGAGUGAUCGAAAG
AUGAAAAGCACUUUGAAAAGAGGGUUAAAUAGCACGUGAAAUUGUUGAAAGGGAAGCGCU
UGUGACCAGACUUGCGCCCGGCGGAUCAUCCGGUGUUCUCACCGGUGCACUCCGCCGGGC
UCAGGCCAGCAUCGGUUCUGGCGGGGGGAUAAAGGCCCAGGGAAUGUGGCUCCUCCGGGA
GUGUUAUAGCCCUGGGUGUAAUACCCUCGCCGGGACCGAGGACCGCGCUCUGCAAGGAUG
CUGGCGUAAUGGUCACCAGCGACCCGUCUUGAAACACGGACCAAGGAGUCAAGGUUUUGC
GCGAGUGUUUGGGUGUAAAACCCGCACGCGUAAUGAAAGUGAACGUAGGUGAGAGCUUCG
GCGCAUCAUCGACCGAUCCUGAUGUAUUCGGAUGGAUUUGAGUAGGAGCGUUAAGCCUUG
GACCCGAAAGAUGGUGAACUAUGCUUGGAUAGGGUGAAGCCAGAGGAAACUCUGGUGGAG
GCUCGCAGCGGUUCUGACGUGCAAAUCGAUCGUCAAAUCUGAGCAUGGGGGCGAAAGACU
AAUCGAACCAUCUAGUAGCUGGUUACCGCCGAAGUUUCCCUCAGGAUAGCAGUGUCGACC
UUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGGGACUCGGGGGCGAUUUUUAGCCUUCAUC
CAUUCUCAAACUUUAAAUAUGUAAGAAGCCCUUGUUACUUAACUGAACGUGGGCAUUCGA
AUGUAUCGACACUAGUGGGCCAUUUUUGGUAAGCAGAACUGGCGAUGCGGGAUGAACCGA
ACGCGGGGUUAAGGUGCCGGAGUGGACGCUCAUCAGACACCACAAAAGGCGUUAGUACAU
CUUGACAGCAGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAAGGACUGUGUAACAACUCA
CCUGCCGAAUGUACUAGCCCUGAAAAUGGAUGGCGCUCAAGCGUCCCACCCAUACCCCGC
CCUCAGGGUAGAAACGAUGCCCUGAGGAGUAGGCGGCCGUGGAGGUCAGUGACGAAGCCU
AGGGCGUGAGCCCGGGUCGAACGGCCUCUAGUGCAGAUCUUGGUGGUAGUAGCAAAUACU
UCAAUGAGAACUUGAAGGACCGAAGUGGGGAAAGGUUCCAUGUGAACAGCGGUUGGACAU
GGGUUAGUCGAUCCUAAGCCAUAGGGAAGUUCCGUUUCAAAGGGGCACUCGUGCCCCGUG
UGGCGAAAGGGAAGCCGGUUAAUAUUCCGGCACCUGGAUGUGGGUUUUGCGCGGCAACGC
AACUGAACGCGGAGACGACGGCGGGGGCCCCGGGCAGAGUUCUCUUUUCUUCUUAACGGU
CUAUCACCCUGGAAACAGUUUGUCUGGAGAUAGGGUUUAAUGGCCGGAAGAGCCCGACAC
UUCUGUCGGGUCCGGUGCGCUCUCGACGUCCCUUGAAAAUCCGCGGGAGGGAAUAAUUCU
CACGCCAGGUCGUACUCAUAACCGCAGCAGGUCCCCAAGGUGAACAGCCUCUGGUUGAUA
GAACAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGUAACUUCGGGAAAAGGAUUGGC
UCUAAGGGUUGGGCACGUUGGGCUUUGGGCGGACGCCCUGGGAGCAGAGGGCCUCUAGCC
GGGCAACCGGCCGGCGGCCCUCAGCACCCGGGGUUGAAGCCCUUAGCAGGCUUCGGCCGU
CCGGCGUGCGGUUAACAACCAACUUAGAACUGGUACGGACAGGGGGAAUCUGACUGUCUA
AUUAAAACAUAGCAUUGCGAUGGCCAGAAAGUGGUGUUGACGCAAUGUGAUUUCUGCCCA
GUGCUCUGAAUGUCAAAGUGAAGAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACU
AUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAU
UAACGAGAUUCCCACUGUCCCUAUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGC
UUGGCAAAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGA
AAAGACAUAGGAGGUGUAGAAUAGGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACUCC
UAUUGUUUUUUUACUUAUUCAAUGAAGCGGGGCUGGACUUGCGUCCAACUUCUGGAGUUA
AGGUCCUUCGCGGGCCGACCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGC
GGCACAUCUGUUAAACCAUAACGCAGGUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUC
UCCAGUAGAACAAAAGGGUAAAAGUCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACC
AUGAAAGUGUGGCCUAUCGAUCCUUUAGUCCCUCGAAAUUUGAGGCUAGAGGUGCCAGAA
AAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUU
GAUCCUUCGAUGUCGGCUCUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUG
UUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUA
CCCUACUGAUGAACUCGUCGCAAUGGUAAUUCAGCUUAGUACGAGAGGAACCGCUGAUUC
AGAUAAUUGGUUUUUGCGGUUGUCCGACCGGGCAGUGCCGCGAAGCUACCAUCUGCUGGA
UAAUGGCUGAACGCCUCUAAGUCAGAAUCCAUGCCAGAACGCGACGAUACUACCCGCACG
UUGUAGACGUAUAAGAAUAGGCUCCGGCCUCGUAUCCUAGCAGGCGAUUCCUCCGCCGGC
CUCGAAGUGGCCGUCGGUAAUUCGCGUAUUGCAAUUUAGACACGCGCGGGAUCAAAUCCU
UUGCAGACGACUUAGAUGUGCGAAAGGGUCCUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGGGUAAGCCCUCCUUCGCCUAGAUUUCCCAG
Sequence of entity 2 (C2), FASTA
>8I9X_2 RNA (319-MER) (chains C2)
AAACUUUCAACAACGGAUCUCUUGGUUCUGGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
AAGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCG
CCGGUAUUCCGGCGGGCAUGCCUGUUCGAGCGUCAUUUCAACCAUCAAGCCCUGGGCUUG
UGUUGGGGACCCGCGGCUGCUCGCGGGCCCUGAAAAGCAGUGGCGGGCUCGCUAGUCACA
CCGAGCGUAGUAGAACUUCUAUUCGAUCUCGCUCAGGGCGUGCGGCGGGUGCCAGCCGUA
AAACCCCAGCUUCUUCUAA
Sequence of entity 3 (CA), FASTA
>8I9X_3 Brix domain-containing protein (chains CA)
MAAVYKTIAKVTGSKEDKDKEDRSNIIAERKNKQRVLVLSSRGVTYRHRHLLNDLASMLP
HGRKDAKFDTKSRLYELCELAELYNCNNVLFFEARKGKDLYMWFSKVPNGPTVKFYAQNL
HTMEELHFQGNCLKGSRPILSFDAAFEQEPYLKVIKELFLHTFGVPQGHKKSKPFIDHVL
SFSVADGKIWVRNYEIREVEKVKGEADKREEGETEKPKAAKPGSKDTDINLIEIGPRFVL
TPIIIQEGSFGGPILYENKRFISPNKIRAELRKAKAARHHARMEQQRDLLARKRQLGLDE
STPKKKDDLDTRELFA
Sequence of entity 4 (CB), FASTA
>8I9X_4 Ribosome biogenesis protein C8F11.04 (chains CB)
MAPSTAVAKKETDAVIPVDPDQTLKACKALLAHIKKAAAAPRPDGKQNLLADEESTVAET
PIWLTLTTKKHIHDSHRLQPGKIILPHPLNTSEEISVCLITADPQRFYKNAVADEFPEDL
RAKIGRVIDISHLKAKFKAYEAQRKLFSEHDVFLADTRIINRLPKALGKTFYKTTTKRPI
PVVLMAQREKVNGKRVPAPKGKKEKRDPLENANARPIPEIVAEIRKAIGAALVHLSPSTN
TAIKVGYANWEPEKLAANIETVIRELVERFVPQKWQNVRNFYVKGPETAALPIYQTDELW
LDESKVVPDGQEPARALPGKREKANIGKKRKPLEDASQPALEETGKDERPKKKAKKTLPE
SNDDKLDKAIAERKEQLKKQKAAAKKVAADI
Sequence of entity 5 (CC), FASTA
>8I9X_5 Ribosome biogenesis protein ERB1 (chains CC)
MGSKIVEKKRKSRDSDSESDNELGDGLFDGVLSQSEDEEDYIPSSEVDEDDDDDADESAS
EDSDDSNDSEDDEVEEDDEALLSDEIPSEGESEKDQDLAESKESKQDQDKEPSEPEILEP
FVDPPRKEDEELEDRNYRIEKDANGGIRYVYDEIDPVYDSDDTDYNVPVNTIGNIPLSFY
DSYPHIGYDINGKKIMRPATGDALQNLLDSIEVPEGWTGLTDPNTGKPLNLSRDELELIR
KVQQGLIPDDVEDPYPDTVEWFTSVEEKMPLSAAPEPKRRFIPSKNEAKQIMKLVRAIRE
GRILPYKPPEEREREELEKEEEFYDLWQNEEPQPPNPMHIPAPKLPPPGYDLSYNPPPEY
LPTKEEREEWEKMDPEDREKDYLPTKYDSLRKVPAWGNFVKERFERCMDLYLAPRVRKNR
LNIDPNSLLPKLPSPDELKPFPTVQQTIFRGHEGRVRSVAIDPTGVALATGGDDGTVRVW
ELLTGRQVWSVKLNGDEAVNTVRWRPTKDTFILAAAAGEDIFLMIPTHPSVTPALDQASR
DILNAGFGHATNGKQQANLPPGKEPPGKWARPGTRLEDEGVLLRITVRSTIKAISWHRRG
DHFATVSPSGQRSSVAIHTLSKHLTQIPFRKLNGLAQTASFHPLRPLFFVATQRSIRCYD
LQKLELVKIVQPGAKWISSFDVHPGGDNLVVGSYDKRLLWHDLDLSNRPYKTMRFHTEAI
RAVRFHKGGLPLFADASDDGSLQIFHGKVPNDQLENPTIVPVKMLKGHKVVNKLGVLDID
WHPREPWCVSAGADGTARLWM
Sequence of entity 6 (CD), FASTA
>8I9X_6 Ribosome biogenesis protein YTM1 (chains CD)
MDAPMEDAPAPVAQVKVIFTTTEPDLELPESKRQLLVPADIRRYGLSRILNSESMLDTGS
IPFDFLINGSFLRSSLEDYLTSNGLSLDTTLTLQYVRSLIPPVYEASFEHDDWVSAVDVL
SATSPAGRWSSAANSSAAVQPGQERVLSASYDGLLRIWNASGSVIATSPSGSHGGHTASI
KAAKFLTSDRLASAGMDRTVRVWKYTESDHFTGELKPTLELYGHTGSVDWLDVDGHSKHI
LTASADGAIGFWSASKASAPEPDASLLPGAHVSKRRKATSSVSTAQRGPLGLWSIHTAPA
TAAIFDPRDRTVAYSASQDHTVRTLDLTTGQVVSTLTLTHPLLSLSALTRAGTTSPLLAA
GTSARHITMVDPRASSATTSVMTLRGHANKVVSLSPSPENEYSLVSGSHDGTCRVWDLRS
VRPATKEEGSLGGVSEPVYVIERESWASKGKKKRPVAGDGCKVFSVVWDKLGIFSGGEDK
KVQVNRGRNIVTEQK
Sequence of entity 7 (CE), FASTA
>8I9X_7 RNA helicase (chains CE)
MASESSKKRKFKDSKGPKPDEAVAKPSKFKKLKRDPTPEERETSDSESGNSDGQHEPDQV
DSDGEDAVSDDGSFDEKVAHQDEDGSRPENGTDLEDVPKNDNLLPPPTNAQEFSELNLSE
KTTKAIAEMGFTKMTEIQRRAIPPALAGKDVLGAAKTGSGKTLAFLIPAVEMLSSLRFKP
RNGTGAIVVTPTRELALQIFGVARELMKYHSQTYGVVIGGANRRAEAEKLGKGVNLLIAT
PGRLLDHLQNTPFVFKNLKSLIIDEADRILEIGFEDEMRQIVKILPKEDRQTMLFSATQT
TKVEDLARISLRPGPLYINVDEEKKYSTVEGLEQGYVVVEADKRFLLLFSFLKKMAKKKI
IVFFSSCNSVKYYSELLQYIDLPVLDLHGKQKQQKRTNTFFEFCNAKSGTLICTDVAARG
LDIPQVDWIVQFDPPDDPRDYIHRVGRTARGNNGKGRSLLFLQPCELGFLAHLKAAKVPV
VEYDFPKNKILNVQSQLEKLISTNYYLNQSAKEGYRSYIHAYASHSLRSVFDVHKLDLVK
VAKSFGFSTPPRVDITLSASLSRDKKPQGRRAYGSQPRQGGRYKKVGDIPDPQPNTFG
Sequence of entity 8 (CF), FASTA
>8I9X_8 Ribosome assembly factor mrt4 (chains CF)
MPKSKRARVYHLIQVNKKGREAKERLFSNIRETIPKYQHCFVFSVDNMRNNYLKDVRHEL
NDCRIFFGKTKLMARALGTTPEEEQADGLHRLTRYLTGTVGLLFTNRDPADIESYFSNLS
QVDFARAGTVAPRTVTVPTGIVYSTGGEVPPEHDVPVSHTLEPELRRLGMPVRMIKGKVC
LGDEKGEASEGYTICKEGEVLDSRQTRLLKLFSICLSEFKVSLLGYWNSASGEVTELEAG
KTRPKREGNRRQAMNGDEIDEDQSSDEDSD
Sequence of entity 9 (CG), FASTA
>8I9X_9 60S ribosome subunit biogenesis protein NIP7 (chains CG)
MRPLTDQEMKIVLDKLANYMTDLKSLIAPLEDGDRYVFRMQKDRVYYVKLSIANIATCVA
RDKLLSLGTCLGKMTKSGKFRLHITALPILAQNARYKIWVKDNGAQPFLYGSNIVKAHVG
RWTEDCPEHSGCVVYNMADIPLGFGVTARSTAEARRLDPTGIVCFRQADCGEYLRDEDTL
FTGA
Sequence of entity 10 (CH), FASTA
>8I9X_10 Nucleolar GTP-binding protein 1 (chains CH)
MTGWKDIPPVPTAQEFIDIVLSRTQRRLPTQIRPGFKISRIRAFYTRKVKFTQETCSEKF
GAIISSFPVLSDQHPFHRDLMNILYDADHFKVALGQISTAKNLIETISRDYVRLLKYAQS
LYQCKQLKRAALGRMATLIKRLKDPLIYLDQVRQHLARLPDINPTTRTLLVAGFPNVGKS
SFVRSVTRADTPVEPYAFTTKSLFVGHLDYKYLRYQVIDTPGILDHPLEEMNTIEMQSVT
ALAHLRAAVLYFMDISEQCGFSLKAQINLFKSIKPLFANKMVFIVLNKMDIKKFEELDPE
MQQEINDLTKSGEVEILRASCATQEGVQEVKNHVCERLLVERVSQKLKAGTHSNGNIGTR
LQEVMARIHVATPMDGTTRETFIPEAVKNLKKYDKNDPNRRVLARDIEEANGGAGVFNVD
LRKDWILENPEWKYDKIPEIFDGKNVYDYIDPDIDAKLQALEEEEERLEKEGFYDEDDDL
PDEEEEEILQKAEYIREQHALIRNEAKMRKSLKNRAIIPRKAVKKPLSQLEDHLDQLGVD
TEAIGLRARAQTAQSSRGRSLVRSRGTTADPDAMDIDDGAASAKERLARSRSRARSVAAT
NRLQDGVQGTTLRSKAERQAKLAQRKMNRMARQGEADRHIHASMPKHLFSGKRTIGKTDR
R
Sequence of entity 11 (CI), FASTA
>8I9X_11 Putative RNA-binding protein (chains CI)
MAAELRKKKSKSAVADADAAISKKEKATKVTKATPKAEKRKAPEEASPVAIKKQKADKDA
VVKKAAVAAEDKIAEKPVKSVLKKETSAKAKEAAKPKKKQEKVEEEEEEALENADAAFGS
DEESELDEQTKALMDTLDDGEESDEDESKQVSTFKKGQDVGKIPTPKKAPQKQTNGDSKP
AGDSQPGVMYIARLPHGFYEHELRGYFSQFGEITRLRVVRNKKTGASRHRAFIEFADAEV
ADIAARTMDKYLLFGHILTCKIVPPAQVHPDLFKGANRRFKVVPWNKMAGRQLERPLSES
QWQVKVAKEEQRRAARAEKLKEMGYEFEAPALKVPKAKPVLENGEEEKKAIETAPAPAVE
EKESKEVAKRQAEEEVEEKAPAPKTKKVKEDKPAKEAATISAPKKGKKSKKTKS
Sequence of entity 12 (CJ), FASTA
>8I9X_12 Pescadillo homolog (chains CJ)
MGKAKKKGKSGAARNYMTRTQAVKKLQLSLPDFRKLCIWKGIYPREPRDRRKVNKSATAS
TTFYYTKDIQYLLHEPLLQKFREQKALEKKISRALGRGDVSNAARLERNANLPEKTGKPR
YTLNHIIRERYPTFQDALRDLDDCLSMLFLFANLPSTTAVPAKMIARCERLCHEFQHYLI
VTHSLRKSFLSIKGIYYQANIQGEDILWLVPYKFNQRIVGDVDFRIMGTFVEFYMTLLGF
VNYRLYTSIGLKYPPKFDQVKDDQGAELAAFSLEGLNLASQNGEQKAITNGEEHGPDPKV
QAEVDKLVAKLREEEQQANGDKTDEKGEENEGDDKPSDAIDKFEPVAPGGDVLPQPSYSS
SDPSQLFANFTFFLSRETPRQPLEFILRAFGCKRIGWDAVLGEGAFTTDESDPRITHQII
DRPVIRAAVSEDGDGEDNQTSQKLAPNGRYPGRIYVQPQWVWDSINDEELKPPELYAPGA
QLPPHLSPFVKPTQGQYDPTKPLEEQQTEAEALEAELEDAQAQQEGSDEESGSEVENDMS
VASDEEDEQEDDFGGFSDEDEEQSDEGSEEGDEEEDDDEEEEATLERQRELEAELAGKAV
SKGKPLDPKVKAKLEAKKALERKKKQEAEELERAKGMLSKKKRKLFEQMQYSNAKKNAED
AKLRAKRRRIEKEMAAKKA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
| ZN | Zinc ion | Zn | 2 |
Primary citation
Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis. Lau, B., Huang, Z., Kellner, N. et al. EMBO Rep (2023) 24:e56910-e56910. DOI 10.15252/embr.202356910 · PubMed
Other PDB entries of the same protein (UniProt G0RXZ3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8I9Z 2.7 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4
- 8IA0 2.7 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Puf6
- 8I9P 3.0 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16
- 8I9R 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP
- 8I9V 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2
- 8I9W 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3
- 8I9Y 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2
- 8I9T 3.6 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1
Browse structure collections
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