9OGY: US2
Megrivirus E 3' internal ribosome entry site (IRES) RNA core region bound to rabbit ribosome. Determined by electron microscopy at 3.28 Å resolution. Released 14 Jan 2026.
- Method
- Electron microscopy
- Resolution
- 3.28 Å
- Organisms
- Oryctolagus cuniculus, Megrivirus E
- Chains
- 36
- Atoms
- 77,254
- Mol. weight
- 1347.71 kDa
- Ligands
- ZN
- Released
- 14 Jan 2026
Explore 9OGY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9OGY contains 178 α-helices and 236 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: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 54-61 | 8 | |
| α-helix | 62-64 | 3 | |
| β-strand | 68 | 1 | 2 |
| α-helix | 70-76 | 7 | |
| α-helix | 81-93 | 13 | |
| β-strand | 98-101 | 4 | 2 |
| β-strand | 108-110 | 3 | 2 |
Chain b: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 5 |
| β-strand | 29-31 | 3 | 5 |
| β-strand | 36-43 | 8 | 6 |
| α-helix | 47-49 | 3 | |
| α-helix | 50-54 | 5 | |
| β-strand | 57 | 1 | 60 |
| α-helix | 63-65 | 3 | |
| β-strand | 66-73 | 8 | 6 |
| α-helix | 75-80 | 6 | |
| α-helix | 97-99 | 3 | |
Chain B: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-21 | 9 | |
| β-strand | 25 | 1 | 3 |
| α-helix | 32-34 | 3 | |
| β-strand | 40-42 | 3 | 3 |
| β-strand | 46-48 | 3 | 3 |
| α-helix | 51-66 | 16 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 4 |
| α-helix | 81-83 | 3 | |
| α-helix | 84-94 | 11 | |
| β-strand | 97-100 | 4 | 4 |
| α-helix | 103-104 | 2 | |
| β-strand | 121-124 | 4 | 4 |
| α-helix | 131-137 | 7 | |
| β-strand | 144-146 | 3 | 4 |
| β-strand | 159 | 1 | 4 |
| α-helix | 168-186 | 19 | |
| α-helix | 207-216 | 10 | |
Chain c: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| α-helix | 20-22 | 3 | |
| β-strand | 32-36 | 5 | 11 |
| β-strand | 43-47 | 5 | 11 |
| β-strand | 55 | 1 | 12 |
| β-strand | 62 | 1 | 12 |
| β-strand | 64-65 | 2 | 13 |
| β-strand | 72-73 | 2 | 13 |
| α-helix | 74 | 1 | |
| β-strand | 78 | 1 | 11 |
| β-strand | 81 | 1 | 11 |
Chain C: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 28-32 | 5 | 7 |
| β-strand | 33-34 | 2 | 8 |
| β-strand | 46-50 | 5 | 7 |
| α-helix | 60-63 | 4 | |
| β-strand | 66-70 | 5 | 8 |
| β-strand | 82-91 | 10 | 8 |
| β-strand | 96-105 | 10 | 8 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-127 | 8 | 9 |
| β-strand | 135-142 | 8 | 9 |
| β-strand | 143 | 1 | 10 |
| α-helix | 144-146 | 3 | |
| α-helix | 158-177 | 20 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-200 | 9 | |
| β-strand | 207 | 1 | 10 |
| β-strand | 211-214 | 4 | 9 |
| β-strand | 215-216 | 2 | 8 |
| β-strand | 217 | 1 | 9 |
| α-helix | 225-229 | 5 | |
Chain d: 0 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-17 | 6 | 18 |
| β-strand | 21 | 1 | 19 |
| β-strand | 27 | 1 | 19 |
| β-strand | 28-34 | 7 | 18 |
| β-strand | 41-46 | 6 | 18 |
| β-strand | 47 | 1 | 33 |
| β-strand | 55-56 | 2 | 18 |
Chain D: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-71 | 7 | |
| α-helix | 79-83 | 5 | |
| α-helix | 93-97 | 5 | |
| β-strand | 103-116 | 14 | 14 |
| β-strand | 119-131 | 13 | 14 |
| β-strand | 137-144 | 8 | 14 |
| α-helix | 147-160 | 14 | |
| β-strand | 162-163 | 2 | 14 |
| β-strand | 168 | 1 | 15 |
| β-strand | 179 | 1 | 15 |
| β-strand | 184-187 | 4 | 16 |
| β-strand | 192-196 | 5 | 16 |
| β-strand | 204 | 1 | 17 |
| α-helix | 208-217 | 10 | |
| β-strand | 222 | 1 | 17 |
| β-strand | 223-227 | 5 | 16 |
| α-helix | 233-245 | 13 | |
| α-helix | 253-255 | 3 | |
| α-helix | 258-259 | 2 | |
| α-helix | 265-268 | 4 | |
| α-helix | 270-274 | 5 | |
Chain e: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| 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 ribosomal RNA | 2 | RNA | 1870 | Oryctolagus cuniculus | |
| Megrivirus E 3' IRES RNA | A | RNA | 270 | Megrivirus E | |
| uS2 (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 | O18789 (AlphaFold model) |
| Ribosomal protein S3 | E | protein | 281 | Oryctolagus cuniculus | G1TNM3 (AlphaFold model) |
| 40S ribosomal protein S4 | F | protein | 263 | Oryctolagus cuniculus | G1TK17 |
| Ribosomal protein S5 | G | protein | 204 | Oryctolagus cuniculus | G1TFM5 |
| 40S ribosomal protein S6 | H | protein | 249 | Oryctolagus cuniculus | G1TM55 |
| eS7 | I | protein | 432 | Oryctolagus cuniculus | G1SVB0 |
| 40S ribosomal protein S8 | J | protein | 208 | Oryctolagus cuniculus | G1TJW1 |
| Ribosomal protein S9 (Predicted) | K | protein | 194 | Oryctolagus cuniculus | B7NZS8 |
24 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>9OGY_1 18S ribosomal RNA (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 (A), FASTA
>9OGY_2 Megrivirus E 3' IRES RNA (chains A)
CUUCAGGGUCUUAGUGUUGUGGGAUACCCUGUCGUACACGUAAAACACCCACCUCCUAGC
UCAUGGAGUUAAAUUGAGUAGCCGUUGGAAUCGGCUAUAUAAAUUAUCCAGGAACCUGUC
GAGUAGUUGACCUUAUGCUUUCACAGACGUGUUUUCUUCCUGAAGCAUUUGGAAUAGUGG
GCUUGGGAAAACCCACCUUGGACUAUACGGCCUGAUAGGGUGCUGUUGCUACCAGCACAG
GUUUCUUGAUCCGUAGCGGGUUGUAAUAUG
Sequence of entity 3 (B), FASTA
>9OGY_3 uS2 (SA) (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQTAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS
Sequence of entity 4 (C), FASTA
>9OGY_4 40S ribosomal protein S3a (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 5 (D), FASTA
>9OGY_5 40S ribosomal protein S2 (chains D)
KEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTR
AGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKP
HTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFA
KATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT
Sequence of entity 6 (E), FASTA
>9OGY_6 Ribosomal protein S3 (chains E)
MSARRRRRRAAFRRRAEPFIPISVREPLPFLSAARGGKMAVQISKKRKFVADGIFKAELN
EFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG
SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKL
RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKK
PLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA
Sequence of entity 7 (F), FASTA
>9OGY_7 40S ribosomal protein S4 (chains F)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG
Sequence of entity 8 (G), FASTA
>9OGY_8 Ribosomal protein S5 (chains G)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR
Sequence of entity 9 (H), FASTA
>9OGY_9 40S ribosomal protein S6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK
Sequence of entity 10 (I), FASTA
>9OGY_10 eS7 (chains I)
EPITNRVFQALTSSDFKQQDGGSFSLSRTHLSGFRSRPRRTTIASAATRPPPIPSRGGSA
PTGTPEGAGASRSSRTVPRLPPQPSGPPRAPRHPGFQRALPSLIRPEPGVRAPLLASAGT
RFKRPASQAVKALSARGLLQPQVQVGPRANRVPQRREPRQHLSGHAPGASEGGSASPTYW
SLGITSWDALGFPLRLGGSSGFRSSVALFRPLSFRRGDLPRSREIWASSSAGAQPGEAMF
SSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIII
FVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTL
TAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTG
KDVNFEFPEFQL
Sequence of entity 11 (J), FASTA
>9OGY_11 40S ribosomal protein S8 (chains J)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK
Sequence of entity 12 (K), FASTA
>9OGY_12 Ribosomal protein S9 (Predicted) (chains K)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
A bicistronic viral genome uses a compact type IV IRES near its 3' end to express a transmembrane protein. Sherlock, M.E., Segar, K.E., Kieft, J.S. Cell Rep (2026) 45:116982-116982. DOI 10.1016/j.celrep.2026.116982 · PubMed
Other PDB entries of the same protein (UniProt G1TLT8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7O7Y 2.2 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
- 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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