7SYM: HCV IRES
Structure of the HCV IRES bound to the 40S ribosomal subunit, head opening. Structure 7(delta dII). Determined by electron microscopy at 4.8 Å resolution. Released 13 Jul 2022.
- Method
- Electron microscopy
- Resolution
- 4.8 Å
- Organisms
- Oryctolagus cuniculus, Hepatitis C virus (isolate 1)
- Chains
- 36
- Atoms
- 78,761
- Mol. weight
- 1389.78 kDa
- Ligands
- ZN
- Released
- 13 Jul 2022
Explore 7SYM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7SYM contains 181 α-helices and 239 β-strands across 34 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 a: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 50 | 1 | 66 |
| α-helix | 52-61 | 10 | |
| α-helix | 62-64 | 3 | |
| β-strand | 67-68 | 2 | 1 |
| α-helix | 70-76 | 7 | |
| α-helix | 81-94 | 14 | |
| β-strand | 98-101 | 4 | 1 |
| β-strand | 108-110 | 3 | 1 |
| α-helix | 111-113 | 3 | |
Chain b: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20 | 1 | 5 |
| β-strand | 31 | 1 | 5 |
| β-strand | 37-43 | 7 | 6 |
| α-helix | 50-55 | 6 | |
| α-helix | 62-65 | 4 | |
| β-strand | 66-72 | 7 | 6 |
| α-helix | 76-80 | 5 | |
| α-helix | 89-93 | 5 | |
| α-helix | 97-99 | 3 | |
Chain B: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-21 | 9 | |
| β-strand | 25 | 1 | 2 |
| β-strand | 38-41 | 4 | 3 |
| β-strand | 47-49 | 3 | 3 |
| α-helix | 51-66 | 16 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 4 |
| α-helix | 84-94 | 11 | |
| α-helix | 96 | 1 | |
| β-strand | 97-100 | 4 | 4 |
| β-strand | 121-124 | 4 | 4 |
| α-helix | 131-137 | 7 | |
| β-strand | 144-148 | 5 | 4 |
| β-strand | 159-162 | 4 | 4 |
| α-helix | 168-186 | 19 | |
| α-helix | 199-201 | 3 | |
| α-helix | 207-216 | 10 | |
Chain c: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 32-36 | 5 | 10 |
| β-strand | 44-47 | 4 | 10 |
| β-strand | 55 | 1 | 11 |
| β-strand | 62 | 1 | 11 |
| β-strand | 78-81 | 4 | 10 |
Chain C: 7 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-26 | 3 | |
| β-strand | 28-34 | 7 | 7 |
| β-strand | 43-50 | 8 | 7 |
| α-helix | 58-61 | 4 | |
| β-strand | 66-70 | 5 | 7 |
| β-strand | 82-91 | 10 | 7 |
| β-strand | 95-105 | 11 | 7 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-121 | 2 | 8 |
| β-strand | 124-128 | 5 | 9 |
| β-strand | 134-138 | 5 | 9 |
| β-strand | 140-143 | 4 | 8 |
| α-helix | 158-176 | 19 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-200 | 9 | |
| β-strand | 207-211 | 5 | 8 |
| β-strand | 214 | 1 | 7 |
| β-strand | 215-217 | 3 | 9 |
| α-helix | 226-231 | 6 | |
Chain d: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| β-strand | 10 | 1 | 16 |
| β-strand | 12-21 | 10 | 17 |
| β-strand | 27-34 | 8 | 17 |
| β-strand | 41-47 | 7 | 17 |
| β-strand | 58 | 1 | 16 |
Chain D: 10 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-71 | 7 | |
| α-helix | 79-84 | 6 | |
| α-helix | 92-97 | 6 | |
| β-strand | 103-115 | 13 | 12 |
| β-strand | 120-131 | 12 | 12 |
| β-strand | 137-144 | 8 | 12 |
| α-helix | 148-159 | 12 | |
| β-strand | 162-163 | 2 | 12 |
| β-strand | 168 | 1 | 13 |
| β-strand | 179 | 1 | 13 |
| β-strand | 185-188 | 4 | 14 |
| β-strand | 191-194 | 4 | 14 |
| β-strand | 195-197 | 3 | 15 |
| β-strand | 204-205 | 2 | 15 |
| α-helix | 208-217 | 10 | |
| β-strand | 221 | 1 | 13 |
| β-strand | 222-224 | 3 | 15 |
| α-helix | 233-245 | 13 | |
| α-helix | 253-255 | 3 | |
| α-helix | 258-259 | 2 | |
| α-helix | 262-264 | 3 | |
| α-helix | 265-273 | 9 | |
Chain e: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 30 | 1 | 22 |
| α-helix | 33-35 | 3 | |
| β-strand | 39 | 1 | 22 |
| α-helix | 40-45 | 6 | |
| α-helix | 47-50 | 4 | |
26 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 | 2 | RNA | 1870 | Oryctolagus cuniculus | |
| 40S ribosomal protein SA | B | protein | 295 | Oryctolagus cuniculus | G1TLT8 (AlphaFold model) |
| 40S ribosomal protein S3a | C | protein | 264 | Oryctolagus cuniculus | G1SS70 (AlphaFold model) |
| 40S ribosomal protein S2 | D | protein | 221 | Oryctolagus cuniculus | G1SV32 (AlphaFold model) |
| uS3 | E | protein | 281 | Oryctolagus cuniculus | G1TNM3 (AlphaFold model) |
| 40S ribosomal protein S4 | F | protein | 263 | Oryctolagus cuniculus | G1TA47 |
| uS7 | G | protein | 204 | Oryctolagus cuniculus | G1TFM5 |
| eS6 | H | protein | 249 | Oryctolagus cuniculus | A0A5K1UJS7 |
| 40S ribosomal protein S7 | I | protein | 432 | Oryctolagus cuniculus | G1SVB0 |
| eS8 | J | protein | 208 | Oryctolagus cuniculus | G1TJW1 |
| uS4 | K | protein | 194 | Oryctolagus cuniculus | B7NZS8 |
| eS10 | L | protein | 149 | Oryctolagus cuniculus | G1T168 |
24 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>7SYM_1 18S rRNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCUCCCCCCGGCCCCGGCCGGGGGGGUGGGCGCCGGCGGCUUUGGUGACUCUAGA
UAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCU
AUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAG
GGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGC
GCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUC
UUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGA
GGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUG
CUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCG
AGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUG
UCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGC
CGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUU
CGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGG
UGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUC
AUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACC
AUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCC
GGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGA
AUUUGGCGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAA
ACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGU
GGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAA
CGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAA
CUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAU
GCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCC
UACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCA
AUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAA
GUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCC
CUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCG
AACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGA
AGGAUCAUUA
Sequence of entity 2 (B), FASTA
>7SYM_2 40S ribosomal protein SA (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQTAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS
Sequence of entity 3 (C), FASTA
>7SYM_3 40S ribosomal protein S3a (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 4 (D), FASTA
>7SYM_4 40S ribosomal protein S2 (chains D)
KEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTR
AGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKP
HTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFA
KATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT
Sequence of entity 5 (E), FASTA
>7SYM_5 uS3 (chains E)
MSARRRRRRAAFRRRAEPFIPISVREPLPFLSAARGGKMAVQISKKRKFVADGIFKAELN
EFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG
SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKL
RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKK
PLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA
Sequence of entity 6 (F), FASTA
>7SYM_6 40S ribosomal protein S4 (chains F)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG
Sequence of entity 7 (G), FASTA
>7SYM_7 uS7 (chains G)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR
Sequence of entity 8 (H), FASTA
>7SYM_8 eS6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK
Sequence of entity 9 (I), FASTA
>7SYM_9 40S ribosomal protein S7 (chains I)
EPITNRVFQALTSSDFKQQDGGSFSLSRTHLSGFRSRPRRTTIASAATRPPPIPSRGGSA
PTGTPEGAGASRSSRTVPRLPPQPSGPPRAPRHPGFQRALPSLIRPEPGVRAPLLASAGT
RFKRPASQAVKALSARGLLQPQVQVGPRANRVPQRREPRQHLSGHAPGASEGGSASPTYW
SLGITSWDALGFPLRLGGSSGFRSSVALFRPLSFRRGDLPRSREIWASSSAGAQPGEAMF
SSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIII
FVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTL
TAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTG
KDVNFEFPEFQL
Sequence of entity 10 (J), FASTA
>7SYM_10 eS8 (chains J)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK
Sequence of entity 11 (K), FASTA
>7SYM_11 uS4 (chains K)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED
Sequence of entity 12 (L), FASTA
>7SYM_12 eS10 (chains L)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Comprehensive structural overview of the HCV IRES-mediated translation initiation pathway. Brown, Z.P., Abaeva, I.S., De, S. et al. To be published.
Other PDB entries of the same protein (UniProt G1TLT8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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- 7OYD 2.3 Å, Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
- 7O7Z 2.4 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
- 8SCB 2.5 Å, Terminating ribosome with SRI-41315
- 9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
- 9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
- 7JQB 2.7 Å, SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
- 8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
- 7ZJW 2.8 Å, Rabbit 80S ribosome as it decodes the Sec-UGA codon
- 9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1
- 9Q7Q 2.86 Å, ABCE1-eRF1-rnc-AMD1C
- 7O80 2.9 Å, Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the…
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