6W2S: Cricket Paralysis Virus 5-UTR IRES
Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1). Determined by electron microscopy at 3.47 Å resolution. Released 22 Apr 2020.
- Method
- Electron microscopy
- Resolution
- 3.47 Å
- Organisms
- Oryctolagus cuniculus, Cricket paralysis virus
- Chains
- 43
- Atoms
- 106,911
- Mol. weight
- 1840.05 kDa
- Ligands
- ZN, MG
- Released
- 22 Apr 2020
Explore 6W2S in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6W2S contains 354 α-helices and 276 β-strands across 41 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 1: 30 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-19 | 10 | |
| α-helix | 24-35 | 12 | |
| α-helix | 47-60 | 14 | |
| α-helix | 64-77 | 14 | |
| α-helix | 84-108 | 25 | |
| α-helix | 111-118 | 8 | |
| α-helix | 125-128 | 4 | |
| α-helix | 137-159 | 23 | |
| α-helix | 160-164 | 5 | |
| α-helix | 173-185 | 13 | |
| α-helix | 194-207 | 14 | |
| α-helix | 222-227 | 6 | |
| α-helix | 228-233 | 6 | |
| α-helix | 235-242 | 8 | |
| α-helix | 246-260 | 15 | |
| α-helix | 261-263 | 3 | |
| α-helix | 267-269 | 3 | |
| α-helix | 273-283 | 11 | |
| α-helix | 289-309 | 21 | |
| α-helix | 315-327 | 13 | |
| α-helix | 346-359 | 14 | |
| α-helix | 369-372 | 4 | |
| α-helix | 379-382 | 4 | |
| α-helix | 391-394 | 4 | |
| α-helix | 407-415 | 9 | |
| α-helix | 428-446 | 19 | |
| β-strand | 449 | 1 | 50 |
| α-helix | 452-458 | 7 | |
| α-helix | 465-476 | 12 | |
| β-strand | 492 | 1 | 50 |
| α-helix | 515-517 | 3 | |
| α-helix | 523-532 | 10 | |
Chain 2: 29 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 333-336 | 4 | |
| α-helix | 343-345 | 3 | |
| α-helix | 351-355 | 5 | |
| β-strand | 363 | 1 | 52 |
| β-strand | 366-367 | 2 | 52 |
| α-helix | 371-383 | 13 | |
| α-helix | 392-394 | 3 | |
| α-helix | 395-413 | 19 | |
| α-helix | 445-460 | 16 | |
| α-helix | 467-473 | 7 | |
| α-helix | 476-488 | 13 | |
| α-helix | 500-510 | 11 | |
| α-helix | 515-518 | 4 | |
| α-helix | 545-554 | 10 | |
| α-helix | 563-575 | 13 | |
| α-helix | 582-592 | 11 | |
| α-helix | 594-597 | 4 | |
| α-helix | 603-623 | 21 | |
| α-helix | 635-638 | 4 | |
| α-helix | 655-661 | 7 | |
| α-helix | 666-667 | 2 | |
| α-helix | 672-673 | 2 | |
| α-helix | 674-684 | 11 | |
| α-helix | 692-694 | 3 | |
| α-helix | 710-713 | 4 | |
| α-helix | 730-740 | 11 | |
| β-strand | 762 | 1 | 53 |
| β-strand | 764 | 1 | 53 |
| α-helix | 769-780 | 12 | |
| α-helix | 800-805 | 6 | |
| α-helix | 810-823 | 14 | |
| β-strand | 831 | 1 | 54 |
| β-strand | 836 | 1 | 54 |
| α-helix | 856-862 | 7 | |
| α-helix | 866-870 | 5 | |
Chain 3: 23 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 33-45 | 13 | |
| α-helix | 52-59 | 8 | |
| α-helix | 77-86 | 10 | |
| α-helix | 97-102 | 6 | |
| α-helix | 105-119 | 15 | |
| α-helix | 125-140 | 16 | |
| α-helix | 146-151 | 6 | |
| α-helix | 163-178 | 16 | |
| α-helix | 183-196 | 14 | |
| α-helix | 204-216 | 13 | |
| α-helix | 225-231 | 7 | |
| α-helix | 253-263 | 11 | |
| α-helix | 271-274 | 4 | |
| α-helix | 282-289 | 8 | |
| α-helix | 295-298 | 4 | |
| α-helix | 307-319 | 13 | |
| α-helix | 330-345 | 16 | |
| β-strand | 352 | 1 | 55 |
| α-helix | 353-360 | 8 | |
| α-helix | 364-377 | 14 | |
| β-strand | 383 | 1 | 56 |
| β-strand | 390 | 1 | 55 |
| β-strand | 392 | 1 | 56 |
| α-helix | 402-409 | 8 | |
| α-helix | 412-416 | 5 | |
| α-helix | 417-419 | 3 | |
Chain 4: 8 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 111-113 | 3 | 59 |
| α-helix | 116-127 | 12 | |
| β-strand | 137-142 | 6 | 60 |
| β-strand | 148-150 | 3 | 59 |
| β-strand | 151-156 | 6 | 60 |
| α-helix | 170-183 | 14 | |
| β-strand | 188-189 | 2 | 60 |
| β-strand | 193-195 | 3 | 60 |
| α-helix | 202-211 | 10 | |
| β-strand | 219-222 | 4 | 60 |
| β-strand | 233-239 | 7 | 60 |
| β-strand | 251-255 | 5 | 60 |
| β-strand | 256-258 | 3 | 59 |
| α-helix | 263-277 | 15 | |
| α-helix | 285-289 | 5 | |
| α-helix | 291-313 | 23 | |
| α-helix | 324-334 | 11 | |
| α-helix | 341-372 | 32 | |
Chain 5: 13 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31 | 1 | 64 |
| β-strand | 37 | 1 | 64 |
| β-strand | 38-41 | 4 | 65 |
| α-helix | 43-49 | 7 | |
| α-helix | 50-52 | 3 | |
| β-strand | 65-68 | 4 | 66 |
| β-strand | 71-72 | 2 | 65 |
| β-strand | 75-78 | 4 | 65 |
| α-helix | 97-110 | 14 | |
| β-strand | 116-121 | 6 | 66 |
| α-helix | 131-143 | 13 | |
| β-strand | 149-151 | 3 | 66 |
| α-helix | 155-157 | 3 | |
| β-strand | 165-167 | 3 | 66 |
| α-helix | 171-175 | 5 | |
| β-strand | 200-201 | 2 | 66 |
| α-helix | 211-214 | 4 | |
| α-helix | 227-232 | 6 | |
| α-helix | 247-270 | 24 | |
| α-helix | 272-275 | 4 | |
| α-helix | 277-288 | 12 | |
| α-helix | 300-303 | 4 | |
| α-helix | 317-348 | 32 | |
Chain 6: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-15 | 12 | |
| α-helix | 29-39 | 11 | |
| α-helix | 44-56 | 13 | |
| α-helix | 64-74 | 11 | |
| α-helix | 82-86 | 5 | |
| α-helix | 99-109 | 11 | |
| α-helix | 114-120 | 7 | |
| α-helix | 134-148 | 15 | |
| β-strand | 150 | 1 | 68 |
| β-strand | 152-154 | 3 | 69 |
| α-helix | 155-162 | 8 | |
| α-helix | 168-175 | 8 | |
| β-strand | 180-182 | 3 | 69 |
| β-strand | 186-188 | 3 | 69 |
| α-helix | 207-214 | 8 | |
Chain 7: 17 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 184-203 | 20 | |
| α-helix | 210-217 | 8 | |
| α-helix | 224-244 | 21 | |
| α-helix | 252-256 | 5 | |
| α-helix | 257-261 | 5 | |
| α-helix | 263-266 | 4 | |
| α-helix | 276-289 | 14 | |
| α-helix | 296-299 | 4 | |
| α-helix | 309-324 | 16 | |
| α-helix | 333-340 | 8 | |
| α-helix | 358-373 | 16 | |
| α-helix | 388-403 | 16 | |
| α-helix | 407-414 | 8 | |
| α-helix | 438-461 | 24 | |
| β-strand | 470-471 | 2 | 68 |
| α-helix | 472-482 | 11 | |
| α-helix | 489-497 | 9 | |
| β-strand | 504-507 | 4 | 68 |
| β-strand | 512-515 | 4 | 68 |
| α-helix | 529-551 | 23 | |
Chain 8: 20 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-22 | 7 | |
| α-helix | 23-25 | 3 | |
| α-helix | 28-31 | 4 | |
| α-helix | 35-38 | 4 | |
| α-helix | 46-53 | 8 | |
| α-helix | 63-71 | 9 | |
| α-helix | 81-84 | 4 | |
| α-helix | 89-93 | 5 | |
| α-helix | 98-105 | 8 | |
| α-helix | 119-130 | 12 | |
| α-helix | 140-147 | 8 | |
| α-helix | 155-171 | 17 | |
| α-helix | 175-192 | 18 | |
| α-helix | 201-213 | 13 | |
| α-helix | 241-246 | 6 | |
| α-helix | 253-256 | 4 | |
| α-helix | 270-287 | 18 | |
| α-helix | 294-301 | 8 | |
| α-helix | 306-318 | 13 | |
| α-helix | 342-367 | 26 | |
33 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 | A | RNA | 1697 | Oryctolagus cuniculus | |
| Crpv 5'-utr ires | 0 | RNA | 377 | Cricket paralysis virus | |
| uS2 | B | protein | 295 | Oryctolagus cuniculus | G1TLT8 (AlphaFold model) |
| eS1 | C | protein | 264 | Oryctolagus cuniculus | G1SS70 (AlphaFold model) |
| uS5 | D | protein | 255 | Oryctolagus cuniculus | G1SWM1 (AlphaFold model) |
| eS4 | F | protein | 263 | Oryctolagus cuniculus | G1TK17 (AlphaFold model) |
| eS6 | H | protein | 249 | Oryctolagus cuniculus | G1TM55 |
| eS7 | I | protein | 194 | Oryctolagus cuniculus | G1SVB0 |
| eS8 | J | protein | 208 | Oryctolagus cuniculus | G1TJW1 |
| uS4 | K | protein | 194 | Oryctolagus cuniculus | B7NZS8 |
| uS17 | M | protein | 158 | Oryctolagus cuniculus | G1TRM4 |
| uS15 | O | protein | 151 | Oryctolagus cuniculus | G1SP51 |
31 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6W2S_1 18S rRNA (chains A)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUG
ACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGUGGUGACUCUAGAUAACCUCGGGCC
GAUCGCACGCCCGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUA
GUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAG
GGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUC
CCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAU
UGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCA
GCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUC
GUAGUUGGAUCUUGGGAGCGGCCGUCCCCUGCUCGGCGCCGGCCCGAAGCGUUUACUUUG
AAAAAAUUAGAGUGUUCAAAGCAGGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAG
GACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGG
GGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAG
CGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGAC
GAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUA
UUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUA
UGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUG
CGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACA
GAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGA
GCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCG
ACCCCGGUCGGCGUAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCA
AUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCU
CAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUG
GGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUA
AGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGG
AUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUGCCCUGGCGGAGCGCUGAGAAG
ACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAAC
CUGCGGAAGGAUCAUUA
Sequence of entity 2 (0), FASTA
>6W2S_2 CrPV 5'-UTR IRES (chains 0)
UUCGAUACCAAGAGCUGGUGUCUGAGGGAUUACGACUCGCGUGGUCGGACAGCACAUGUU
AGUCAUGUAUUAUGGUGUUUCCCAACACGUAUCUUUGCUCUAGUAUUGAACUUUAGUGAU
GAGUGUACUUGGCAUGUACACCUGAUUAGUUAGCCCUUGUGGAUACGCCACUGCCGCUCA
GGUACAGUAGGACAUACCCCAAAUAUUGGGUUUUUUUUUUAGAGAAGAAAAUUAGUGGCG
AAACGUACGGUUUAUGUCAAAGGAGAAGGUGAUUUUAAUUGCACCUGAAGCAACCCUAGG
UCUUCCCUUUGAUGUGAGCUAAUAAGGAGUAACCGAUUCUUACAAUGUGAUCAUGUCUUU
UCAACAAACAAAGGAUC
Sequence of entity 3 (B), FASTA
>6W2S_3 uS2 (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQTAFREPR
LLVVTDPQADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAQ
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPEPEFTA
TQPEVADWSEGMQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWMGTTTEWS
Sequence of entity 4 (C), FASTA
>6W2S_4 eS1 (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 5 (D), FASTA
>6W2S_5 uS5 (chains D)
MADDAGAAGGPGGPGGPGNKEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFL
GAALKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGLKCSKEVATAIRGAIILA
KLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLLMAG
IDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTNHLMKTHT
RVSVQRTQAPAVATT
Sequence of entity 6 (F), FASTA
>6W2S_6 eS4 (chains F)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG
Sequence of entity 7 (H), FASTA
>6W2S_7 eS6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK
Sequence of entity 8 (I), FASTA
>6W2S_8 eS7 (chains I)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL
Sequence of entity 9 (J), FASTA
>6W2S_9 eS8 (chains J)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK
Sequence of entity 10 (K), FASTA
>6W2S_10 uS4 (chains K)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED
Sequence of entity 11 (M), FASTA
>6W2S_11 uS17 (chains M)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF
Sequence of entity 12 (O), FASTA
>6W2S_12 uS15 (chains O)
MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGV
AQVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIES
RIHRLARYYKTKRVLPPNWKYESSTASALVA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
| MG | Magnesium ion | Mg | 1 |
Primary citation
A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate. Neupane, R., Pisareva, V.P., Rodriguez, C.F. et al. Elife (2020) 9. DOI 10.7554/eLife.54575 · 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…
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- 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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