8G6J: 40S ribosomal protein S3a
mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2). Determined by electron microscopy at 2.8 Å resolution. Released 19 Apr 2023.
- Method
- Electron microscopy
- Resolution
- 2.8 Å
- Organism
- Homo sapiens
- Chains
- 86
- Atoms
- 225,765
- Mol. weight
- 4006.57 kDa
- Ligands
- YRB, GSP, MET, PHE
- Released
- 19 Apr 2023
Explore 8G6J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8G6J contains 619 α-helices and 609 β-strands across 79 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 EF: 14 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-14 | 9 | 55 |
| α-helix | 20-31 | 12 | |
| α-helix | 36-49 | 14 | |
| α-helix | 57-59 | 3 | |
| α-helix | 64-69 | 6 | |
| β-strand | 76-81 | 6 | 55 |
| β-strand | 85-91 | 7 | 55 |
| α-helix | 99-107 | 9 | |
| β-strand | 111-117 | 7 | 55 |
| α-helix | 122-127 | 6 | |
| α-helix | 133-142 | 10 | |
| β-strand | 148-153 | 6 | 55 |
| α-helix | 155-157 | 3 | |
| α-helix | 164-181 | 18 | |
| α-helix | 185-187 | 3 | |
| β-strand | 189-192 | 4 | 55 |
| β-strand | 194 | 1 | 56 |
| β-strand | 199 | 1 | 56 |
| β-strand | 214-218 | 5 | 57 |
| β-strand | 221-225 | 5 | 57 |
| α-helix | 228-233 | 6 | |
| α-helix | 235-240 | 6 | |
| β-strand | 247 | 1 | 58 |
| β-strand | 248-249 | 2 | 59 |
| β-strand | 250-256 | 7 | 60 |
| β-strand | 260-266 | 7 | 60 |
| β-strand | 269 | 1 | 58 |
| β-strand | 272 | 1 | 61 |
| β-strand | 277-281 | 5 | 59 |
| β-strand | 285-288 | 4 | 59 |
| β-strand | 289-294 | 6 | 60 |
| β-strand | 297-299 | 3 | 60 |
| β-strand | 302 | 1 | 61 |
| β-strand | 307-312 | 6 | 60 |
| β-strand | 325-328 | 4 | 59 |
| β-strand | 337-346 | 10 | 62 |
| β-strand | 353 | 1 | 63 |
| α-helix | 359 | 1 | |
| β-strand | 360-363 | 4 | 62 |
| β-strand | 366-379 | 14 | 62 |
| β-strand | 388-389 | 2 | 62 |
| β-strand | 394 | 1 | 63 |
| β-strand | 399-406 | 8 | 62 |
| α-helix | 419-422 | 4 | |
| β-strand | 424-428 | 5 | 62 |
| β-strand | 431-443 | 13 | 62 |
Chain La: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 7-10 | 4 | |
| α-helix | 42-48 | 7 | |
| β-strand | 72-73 | 2 | 193 |
| α-helix | 78-81 | 4 | |
| α-helix | 84-91 | 8 | |
| β-strand | 97-98 | 2 | 178 |
| β-strand | 100-102 | 3 | 194 |
| β-strand | 110-111 | 2 | 193 |
| β-strand | 123-126 | 4 | 194 |
| β-strand | 128-129 | 2 | 193 |
| α-helix | 131-139 | 9 | |
| β-strand | 143-146 | 4 | 194 |
Chain LA: 12 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| α-helix | 10-12 | 3 | |
| α-helix | 14-16 | 3 | |
| α-helix | 29-32 | 4 | |
| α-helix | 34-38 | 5 | |
| β-strand | 40-49 | 10 | 105 |
| β-strand | 58-64 | 7 | 105 |
| β-strand | 71-77 | 7 | 105 |
| β-strand | 79 | 1 | 106 |
| β-strand | 83 | 1 | 25 |
| β-strand | 87-91 | 5 | 105 |
| β-strand | 101-103 | 3 | 105 |
| α-helix | 108 | 1 | |
| β-strand | 112-114 | 3 | 105 |
| β-strand | 116 | 1 | 107 |
| β-strand | 126 | 1 | 107 |
| β-strand | 134-140 | 7 | 105 |
| β-strand | 145-149 | 5 | 105 |
| β-strand | 155-159 | 5 | 105 |
| β-strand | 163-166 | 4 | 105 |
| α-helix | 168 | 1 | |
| β-strand | 169 | 1 | 106 |
| 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 | 108 |
| α-helix | 229-230 | 2 | |
| β-strand | 237-238 | 2 | 108 |
Chain Lb: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-18 | 7 | |
| α-helix | 22-24 | 3 | |
| α-helix | 37-48 | 12 | |
| α-helix | 49-51 | 3 | |
| α-helix | 54-74 | 21 | |
| α-helix | 92-100 | 9 | |
| α-helix | 106-115 | 10 | |
Chain LB: 21 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-16 | 3 | |
| α-helix | 32-35 | 4 | |
| α-helix | 40 | 1 | |
| β-strand | 42-43 | 2 | 111 |
| β-strand | 45-60 | 16 | 112 |
| β-strand | 70-80 | 11 | 112 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-95 | 12 | 113 |
| β-strand | 98-106 | 9 | 113 |
| α-helix | 112-115 | 4 | |
| α-helix | 116-118 | 3 | |
| α-helix | 122-124 | 3 | |
| α-helix | 134-137 | 4 | |
| α-helix | 140-156 | 17 | |
| β-strand | 159-165 | 7 | 113 |
| α-helix | 168-170 | 3 | |
| α-helix | 178-179 | 2 | |
| β-strand | 180-184 | 5 | 113 |
| β-strand | 185-186 | 2 | 111 |
| α-helix | 190-199 | 10 | |
| β-strand | 201 | 1 | 113 |
| β-strand | 204-205 | 2 | 113 |
| α-helix | 207-209 | 3 | |
| β-strand | 216-222 | 7 | 112 |
| α-helix | 223-225 | 3 | |
| β-strand | 227-229 | 3 | 114 |
| α-helix | 231-234 | 4 | |
| α-helix | 237-241 | 5 | |
| β-strand | 270-272 | 3 | 114 |
| β-strand | 276-288 | 13 | 112 |
| β-strand | 292-294 | 3 | 115 |
| β-strand | 297-299 | 3 | 115 |
| α-helix | 316 | 1 | |
| β-strand | 320 | 1 | 116 |
| β-strand | 324 | 1 | 116 |
| β-strand | 330-334 | 5 | 112 |
| β-strand | 344-349 | 6 | 112 |
| α-helix | 357-360 | 4 | |
| α-helix | 361-363 | 3 | |
| β-strand | 365-368 | 4 | 112 |
| α-helix | 382-389 | 8 | |
| α-helix | 393-402 | 10 | |
Chain Lc: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-24 | 15 | |
| β-strand | 26-29 | 4 | 142 |
| α-helix | 31-40 | 10 | |
| β-strand | 45-48 | 4 | 142 |
| α-helix | 54-67 | 14 | |
| β-strand | 70-73 | 4 | 142 |
| α-helix | 78-84 | 7 | |
| β-strand | 93-98 | 6 | 142 |
Chain LC: 24 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-11 | 5 | 122 |
| β-strand | 17-23 | 7 | 122 |
| α-helix | 24-25 | 2 | |
| α-helix | 26-29 | 4 | |
| α-helix | 34-44 | 11 | |
| α-helix | 49-51 | 3 | |
| β-strand | 65-66 | 2 | 123 |
| β-strand | 77-78 | 2 | 123 |
| β-strand | 90 | 1 | 123 |
| α-helix | 100-101 | 2 | |
| α-helix | 117-131 | 15 | |
| α-helix | 134-139 | 6 | |
| β-strand | 152-154 | 3 | 122 |
| α-helix | 156-160 | 5 | |
| α-helix | 164-173 | 10 | |
| α-helix | 177-186 | 10 | |
| β-strand | 188-189 | 2 | 124 |
| α-helix | 190-191 | 2 | |
| α-helix | 193-197 | 5 | |
| β-strand | 201-202 | 2 | 124 |
| β-strand | 208-211 | 4 | 122 |
| α-helix | 217-221 | 5 | |
| β-strand | 228-231 | 4 | 122 |
| α-helix | 237-240 | 4 | |
| α-helix | 242-244 | 3 | |
| β-strand | 250-253 | 4 | 122 |
| α-helix | 254-258 | 5 | |
| α-helix | 260-263 | 4 | |
| α-helix | 279-282 | 4 | |
| α-helix | 289-294 | 6 | |
| α-helix | 296-299 | 4 | |
| α-helix | 303-305 | 3 | |
| α-helix | 311-313 | 3 | |
| α-helix | 322-328 | 7 | |
| α-helix | 332-367 | 36 | |
Chain Ld: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-28 | 8 | 147 |
| α-helix | 29-32 | 4 | |
| α-helix | 38-40 | 3 | |
| α-helix | 41-57 | 17 | |
| β-strand | 62-64 | 3 | 147 |
| α-helix | 66-72 | 7 | |
| β-strand | 83-92 | 10 | 147 |
| β-strand | 102-108 | 7 | 147 |
| β-strand | 120-122 | 3 | 147 |
71 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 |
|---|
| 18S rRNA | S2 | RNA | 1869 | Homo sapiens | |
| 5.8S rRNA | L8 | RNA | 156 | Homo sapiens | |
| 28S rRNA | L5 | RNA | 5069 | Homo sapiens | |
| 5S rRNA | L7 | RNA | 120 | Homo sapiens | |
| 40S ribosomal protein S3a | SB | protein | 264 | Homo sapiens | P61247 (AlphaFold model) |
| 40S ribosomal protein SA | SA | protein | 295 | Homo sapiens | P08865 (AlphaFold model) |
| 40S ribosomal protein S3 | SD | protein | 243 | Homo sapiens | P23396 (AlphaFold model) |
| 40S ribosomal protein S9 | SJ | protein | 194 | Homo sapiens | P46781 (AlphaFold model) |
| 40S ribosomal protein S4, X isoform | SE | protein | 263 | Homo sapiens | P62701 |
| 40S ribosomal protein S2 | SC | protein | 293 | Homo sapiens | P15880 |
| 40S ribosomal protein S6 | SG | protein | 249 | Homo sapiens | P62753 |
| 40S ribosomal protein S5 | SF | protein | 204 | Homo sapiens | P46782 |
74 more molecules are not listed.
Sequence of entity 1 (S2), FASTA
>8G6J_1 18S rRNA (chains S2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGXGGUGCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCGGAA
GGAUCAUUA
Sequence of entity 2 (L8), FASTA
>8G6J_2 5.8S rRNA (chains L8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU
Sequence of entity 3 (L5), FASTA
>8G6J_3 28S rRNA (chains L5)
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
CGGGAGCGGCGGGGGCGGCGCGCGCGCGCGCGCGUGUGGUGUGCGUCGGAGGGCGGCGGC
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 (L7), FASTA
>8G6J_4 5S rRNA (chains L7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
Sequence of entity 5 (SB), FASTA
>8G6J_5 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 6 (SA), FASTA
>8G6J_6 40S ribosomal protein SA (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS
Sequence of entity 7 (SD), FASTA
>8G6J_7 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA
Sequence of entity 8 (SJ), FASTA
>8G6J_8 40S ribosomal protein S9 (chains SJ)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED
Sequence of entity 9 (SE), FASTA
>8G6J_9 40S ribosomal protein S4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG
Sequence of entity 10 (SC), FASTA
>8G6J_10 40S ribosomal protein S2 (chains SC)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
Sequence of entity 11 (SG), FASTA
>8G6J_11 40S ribosomal protein S6 (chains SG)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK
Sequence of entity 12 (SF), FASTA
>8G6J_12 40S ribosomal protein S5 (chains SF)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| YRB | (3R,6R,9S,12S,15S,18S,20R,24aR)-6-[(2S)-butan-2-yl]-3,12-bis[(1R)-1-hydroxy-2-m… | C40 H71 N7 O9 | 1 |
| GSP | 5'-guanosine-diphosphate-monothiophosphate | C10 H16 N5 O13 P3 S | 1 |
| MET | Methionine | C5 H11 N O2 S | 1 |
| PHE | Phenylalanine | C9 H11 N O2 | 1 |
| ZN | Zinc ion | Zn | 8 |
| HMT | (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cep… | C29 H39 N O9 | 1 |
| 3HE | 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2… | C15 H23 N O4 | 1 |
| PUT | 1,4-diaminobutane | C4 H12 N2 | 8 |
| MG | Magnesium ion | Mg | 337 |
| SPD | Spermidine | C7 H19 N3 | 10 |
Water and common crystallization additives (K) are not listed.
Primary citation
mRNA decoding in human is kinetically and structurally distinct from bacteria. Holm, M., Natchiar, S.K., Rundlet, E.J. et al. Nature (2023) 617:200-207. DOI 10.1038/s41586-023-05908-w · PubMed
Other PDB entries of the same protein (UniProt P61247 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
- 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
- 7R4X 2.15 Å, Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map
- 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)
- 8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline
- 9O3V 2.2 Å, Human 80S ribosome stalled on MYC nascent chain
Browse structure collections
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