8RG0: PDB entry 8RG0
Structure of human eIF3 core from closed 48S translation initiation complex. Determined by electron microscopy at 3.4 Å resolution. Released 14 Aug 2024.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Homo sapiens
- Chains
- 19
- Atoms
- 31,348
- Mol. weight
- 1428.92 kDa
- Ligands
- ZN, MG
- Released
- 14 Aug 2024
Explore 8RG0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8RG0 contains 195 α-helices and 89 β-strands across 17 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: 13 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-16 | 14 | |
| α-helix | 27-38 | 12 | |
| α-helix | 44-56 | 13 | |
| α-helix | 63-74 | 12 | |
| α-helix | 81-87 | 7 | |
| α-helix | 91-95 | 5 | |
| α-helix | 97-110 | 14 | |
| α-helix | 115-120 | 6 | |
| α-helix | 126-130 | 5 | |
| α-helix | 134-149 | 16 | |
| β-strand | 153 | 1 | 1 |
| α-helix | 155-161 | 7 | |
| α-helix | 167-177 | 11 | |
| β-strand | 181 | 1 | 1 |
| β-strand | 187 | 1 | 1 |
| α-helix | 211-215 | 5 | |
Chain 4: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 91-94 | 4 | 2 |
| α-helix | 96-108 | 13 | |
| α-helix | 109-111 | 3 | |
| β-strand | 118-125 | 8 | 3 |
| β-strand | 128-135 | 8 | 3 |
| α-helix | 150-163 | 14 | |
| β-strand | 168-174 | 7 | 3 |
| α-helix | 181-193 | 13 | |
| β-strand | 199-202 | 4 | 3 |
| β-strand | 213-216 | 4 | 3 |
| β-strand | 217 | 1 | 4 |
| β-strand | 233 | 1 | 4 |
| β-strand | 236-239 | 4 | 2 |
| α-helix | 245-257 | 13 | |
| α-helix | 266-293 | 28 | |
| α-helix | 302-314 | 13 | |
| α-helix | 320-355 | 36 | |
Chain 5: 28 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-76 | 27 | |
| α-helix | 81-92 | 12 | |
| α-helix | 93-99 | 7 | |
| α-helix | 100-106 | 7 | |
| α-helix | 111-114 | 4 | |
| α-helix | 119-122 | 4 | |
| α-helix | 126-143 | 18 | |
| α-helix | 150-168 | 19 | |
| α-helix | 180-202 | 23 | |
| α-helix | 204-206 | 3 | |
| α-helix | 209-217 | 9 | |
| α-helix | 224-238 | 15 | |
| α-helix | 240-248 | 9 | |
| α-helix | 253-256 | 4 | |
| α-helix | 259-262 | 4 | |
| α-helix | 264-284 | 21 | |
| α-helix | 287-292 | 6 | |
| α-helix | 304-307 | 4 | |
| α-helix | 309-325 | 17 | |
| α-helix | 329-350 | 22 | |
| α-helix | 354-377 | 24 | |
| α-helix | 384-402 | 19 | |
| α-helix | 406-416 | 11 | |
| α-helix | 425-426 | 2 | |
| α-helix | 438-464 | 27 | |
| β-strand | 469-471 | 3 | 5 |
| α-helix | 472-478 | 7 | |
| α-helix | 483-497 | 15 | |
| β-strand | 499-501 | 3 | 6 |
| β-strand | 512-514 | 3 | 6 |
| β-strand | 520-524 | 5 | 5 |
| β-strand | 527-531 | 5 | 5 |
| α-helix | 540-559 | 20 | |
Chain 6: 21 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-40 | 25 | |
| α-helix | 44-53 | 10 | |
| α-helix | 60-74 | 15 | |
| α-helix | 81-92 | 12 | |
| α-helix | 97-110 | 14 | |
| α-helix | 116-129 | 14 | |
| α-helix | 134-144 | 11 | |
| α-helix | 156-171 | 16 | |
| α-helix | 175-191 | 17 | |
| α-helix | 192-194 | 3 | |
| α-helix | 196-199 | 4 | |
| α-helix | 201-212 | 12 | |
| α-helix | 222-226 | 5 | |
| α-helix | 238-244 | 7 | |
| α-helix | 250-254 | 5 | |
| α-helix | 255-259 | 5 | |
| α-helix | 270-287 | 18 | |
| β-strand | 292-293 | 2 | 7 |
| α-helix | 294-300 | 7 | |
| α-helix | 305-307 | 3 | |
| α-helix | 308-317 | 10 | |
| β-strand | 322-325 | 4 | 7 |
| β-strand | 331-335 | 5 | 7 |
| α-helix | 343-368 | 26 | |
Chain 8: 11 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32 | 1 | 8 |
| β-strand | 36 | 1 | 8 |
| α-helix | 43-54 | 12 | |
| β-strand | 65-68 | 4 | 9 |
| β-strand | 72 | 1 | 10 |
| β-strand | 75 | 1 | 10 |
| β-strand | 80-82 | 3 | 9 |
| α-helix | 84-86 | 3 | |
| α-helix | 93-106 | 14 | |
| β-strand | 119-122 | 4 | 9 |
| α-helix | 131-143 | 13 | |
| β-strand | 150-152 | 3 | 9 |
| β-strand | 164-166 | 3 | 9 |
| β-strand | 168-169 | 2 | 11 |
| α-helix | 171-177 | 7 | |
| β-strand | 198-199 | 2 | 11 |
| α-helix | 212-224 | 13 | |
| α-helix | 229-235 | 7 | |
| α-helix | 236-240 | 5 | |
| α-helix | 248-286 | 39 | |
| α-helix | 295-303 | 9 | |
| α-helix | 309-349 | 41 | |
Chain H: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-17 | 5 | |
| β-strand | 32-36 | 5 | 12 |
| β-strand | 44-47 | 4 | 12 |
| β-strand | 55 | 1 | 13 |
| β-strand | 62 | 1 | 13 |
| β-strand | 64-65 | 2 | 14 |
| β-strand | 72-73 | 2 | 14 |
| α-helix | 74 | 1 | |
| β-strand | 78-81 | 4 | 12 |
Chain I: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-23 | 2 | |
| α-helix | 30-41 | 12 | |
| α-helix | 47-56 | 10 | |
| α-helix | 63-67 | 5 | |
| α-helix | 71-77 | 7 | |
| α-helix | 86-103 | 18 | |
Chain M: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 96-98 | 3 | 15 |
| α-helix | 100-105 | 6 | |
| β-strand | 117-119 | 3 | 15 |
| α-helix | 130-131 | 2 | |
9 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 |
|---|
| Eukaryotic translation initiation factor 3 subunit K | 3 | protein | 218 | Homo sapiens | Q9UBQ5 (AlphaFold model) |
| Eukaryotic translation initiation factor 3 subunit F | 4 | protein | 357 | Homo sapiens | O00303 (AlphaFold model) |
| Eukaryotic translation initiation factor 3 subunit L | 5 | protein | 564 | Homo sapiens | Q9Y262 (AlphaFold model) |
| Eukaryotic translation initiation factor 3 subunit M | 6 | protein | 374 | Homo sapiens | Q7L2H7 (AlphaFold model) |
| mRNA | 7 | RNA | 255 | Homo sapiens | |
| Eukaryotic translation initiation factor 3 subunit H | 8 | protein | 352 | Homo sapiens | O15372 |
| 18S rRNA | A | RNA | 1869 | Homo sapiens | |
| 40S ribosomal protein S27 | H | protein | 84 | Homo sapiens | P42677 |
| 40S ribosomal protein S13 | I | protein | 151 | Homo sapiens | P62277 |
| 40S ribosomal protein S17 | M | protein | 135 | Homo sapiens | P08708 |
| 40S ribosomal protein SA | N | protein | 295 | Homo sapiens | P08865 |
| 40S ribosomal protein S3a | O | protein | 264 | Homo sapiens | P61247 |
7 more molecules are not listed.
Sequence of entity 1 (3), FASTA
>8RG0_1 Eukaryotic translation initiation factor 3 subunit K (chains 3)
MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAF
FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQA
LDENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWS
ADESGQIFICSQEESIKPKNIVEKIDFDSVSSIMASSQ
Sequence of entity 2 (4), FASTA
>8RG0_2 Eukaryotic translation initiation factor 3 subunit F (chains 4)
MATPAVPVSAPPATPTPVPAAAPASVPAPTPAPAAAPVPAAAPASSSDPAAAAAATAAPG
QTPASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTL
LGTVDKHSVEVTNCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDIT
EHSVLIHEYYSREAPNPIHLTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYA
YYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSA
DNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL
Sequence of entity 3 (5), FASTA
>8RG0_3 Eukaryotic translation initiation factor 3 subunit L (chains 5)
MSYPADDYESEAAYDPYAYPSDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFH
KTVSDLIDQKVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAP
QVGNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPN
QWLWDIIDEFIYQFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVLNVLHSLVDKSNI
NRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENIELN
KKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMI
NKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYSCPKF
LSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLD
LTEQEFRIQLLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYG
DFFIRQIHKFEELNRTLKKMGQRP
Sequence of entity 4 (6), FASTA
>8RG0_4 Eukaryotic translation initiation factor 3 subunit M (chains 6)
MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDV
ESVMNSVVSLLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVR
YTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDA
ASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDL
LTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQE
LQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQN
LNKVKNSLLSLSDT
Sequence of entity 5 (7), FASTA
>8RG0_5 mRNA (chains 7)
GGGCAACAACAACAAGCUAGCCACAACAACAACAACAACAACAACAAGUCGACCAACAAC
AACAACAACAACAACAACAACUCGAGCAACAACAACAACAACAACAACAACAAGGAUCCA
AAACAGACCACCAUGGUACGUUUCAAGGCUUGAGCCCUCGUCACUGCCCUGUGGGGCAAG
GUGACUCUGGAAGAAGUUGGUGGUGAGGCCCUGGGCAGGCUGCAGAGUGUGAGGGAAGGU
CUGGUUGUCUACCAA
Sequence of entity 6 (8), FASTA
>8RG0_6 Eukaryotic translation initiation factor 3 subunit H (chains 8)
MASRKEGTGSTATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGT
EVVQGVLLGLVVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWY
QSTYYGSFVTRALLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEK
DFSPEALKKANITFEYMFEEVPIVIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLG
KNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPEED
LSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN
Sequence of entity 7 (A), FASTA
>8RG0_7 18S rRNA (chains A)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUG
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA
Sequence of entity 8 (H), FASTA
>8RG0_8 40S ribosomal protein S27 (chains H)
MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS
TVLCQPTGGKARLTEGCSFRRKQH
Sequence of entity 9 (I), FASTA
>8RG0_9 40S ribosomal protein S13 (chains I)
MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGV
AQVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIES
RIHRLARYYKTKRVLPPNWKYESSTASALVA
Sequence of entity 10 (M), FASTA
>8RG0_10 40S ribosomal protein S17 (chains M)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGPV
Sequence of entity 11 (N), FASTA
>8RG0_11 40S ribosomal protein SA (chains N)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS
Sequence of entity 12 (O), FASTA
>8RG0_12 40S ribosomal protein S3a (chains O)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
| MG | Magnesium ion | Mg | 1 |
Primary citation
Structural basis for translational control by the human 48S initiation complex. Petrychenko, V., Yi, S.H., Liedtke, D. et al. Nat Struct Mol Biol (2025) 32:62-72. DOI 10.1038/s41594-024-01378-4 · PubMed
Other PDB entries of the same protein (UniProt Q9UBQ5 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1RZ4 2.1 Å, Crystal Structure of Human eIF3k
- 8PPL 2.65 Å, MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
- 28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
- 6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
- 8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
- 8PJ6 2.9 Å, Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and…
- 28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
- 6ZON 3.0 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
- 9KZU 3.0 Å, Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome…
- 8PJ4 3.2 Å, Structure of human 48S translation initiation complex after eIF5 release (48S-4)
- 9KN5 3.2 Å, Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3
- 9KRP 3.2 Å, Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3
Browse structure collections
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