7JQB: SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex. Determined by electron microscopy at 2.7 Å resolution. Released 2 Dec 2020.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organisms
- Oryctolagus cuniculus, Severe acute respiratory syndrome coronavirus 2
- Chains
- 34
- Atoms
- 74,976
- Mol. weight
- 1228.68 kDa
- Released
- 2 Dec 2020
Explore 7JQB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7JQB contains 205 α-helices and 244 β-strands across 33 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, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 47 | 1 | 1 |
| β-strand | 50 | 1 | 2 |
| α-helix | 55-58 | 4 | |
| α-helix | 62-64 | 3 | |
| β-strand | 67-68 | 2 | 3 |
| α-helix | 70-77 | 8 | |
| β-strand | 79 | 1 | 1 |
| α-helix | 81-93 | 13 | |
| β-strand | 98-102 | 5 | 3 |
| β-strand | 107-110 | 4 | 3 |
Chain b: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 14 |
| β-strand | 29-31 | 3 | 14 |
| β-strand | 36-43 | 8 | 15 |
| α-helix | 49-55 | 7 | |
| α-helix | 63-65 | 3 | |
| β-strand | 66-73 | 8 | 15 |
| α-helix | 75-80 | 6 | |
| α-helix | 96-99 | 4 | |
Chain B: 13 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 10-11 | 2 | |
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 11 |
| α-helix | 33-37 | 5 | |
| β-strand | 38-41 | 4 | 11 |
| β-strand | 47-49 | 3 | 11 |
| α-helix | 51-66 | 16 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 12 |
| α-helix | 84-94 | 11 | |
| β-strand | 97-100 | 4 | 12 |
| β-strand | 121-124 | 4 | 12 |
| α-helix | 131-136 | 6 | |
| β-strand | 144-148 | 5 | 12 |
| β-strand | 159-162 | 4 | 12 |
| α-helix | 168-185 | 18 | |
| α-helix | 194-195 | 2 | |
| α-helix | 199-202 | 4 | |
| α-helix | 204-206 | 3 | |
| α-helix | 207-214 | 8 | |
Chain c: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-20 | 11 | |
| α-helix | 21-23 | 3 | |
| α-helix | 25-31 | 7 | |
| α-helix | 34-37 | 4 | |
| β-strand | 46-55 | 10 | 27 |
| α-helix | 56-57 | 2 | |
| β-strand | 58 | 1 | 28 |
| β-strand | 66 | 1 | 28 |
| β-strand | 69-74 | 6 | 27 |
| β-strand | 80-84 | 5 | 27 |
| β-strand | 100-104 | 5 | 27 |
| β-strand | 120-125 | 6 | 27 |
| α-helix | 130-134 | 5 | |
Chain C: 10 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-26 | 3 | |
| β-strand | 28-34 | 7 | 16 |
| β-strand | 43-50 | 8 | 16 |
| β-strand | 53 | 1 | 17 |
| β-strand | 56 | 1 | 17 |
| β-strand | 66-70 | 5 | 16 |
| α-helix | 71-73 | 3 | |
| β-strand | 82-91 | 10 | 16 |
| β-strand | 96-105 | 10 | 16 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-125 | 6 | 16 |
| β-strand | 128 | 1 | 16 |
| β-strand | 134-142 | 9 | 16 |
| β-strand | 143 | 1 | 18 |
| α-helix | 144-146 | 3 | |
| α-helix | 155-157 | 3 | |
| α-helix | 158-177 | 20 | |
| α-helix | 181-186 | 6 | |
| α-helix | 192-200 | 9 | |
| α-helix | 201-203 | 3 | |
| β-strand | 207 | 1 | 18 |
| β-strand | 211-219 | 9 | 16 |
| α-helix | 225-231 | 7 | |
Chain d: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-21 | 12 | 26 |
| β-strand | 27-34 | 8 | 26 |
| β-strand | 43-44 | 2 | 26 |
| β-strand | 46-47 | 2 | 26 |
| β-strand | 55-58 | 4 | 26 |
Chain D: 11 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-71 | 7 | |
| α-helix | 79-84 | 6 | |
| α-helix | 94-98 | 5 | |
| β-strand | 103-115 | 13 | 20 |
| β-strand | 120-131 | 12 | 20 |
| β-strand | 136-137 | 2 | 21 |
| β-strand | 138-144 | 7 | 20 |
| α-helix | 147-160 | 14 | |
| β-strand | 163-164 | 2 | 21 |
| β-strand | 168 | 1 | 22 |
| β-strand | 179 | 1 | 22 |
| β-strand | 184-188 | 5 | 23 |
| β-strand | 191-197 | 7 | 23 |
| β-strand | 204-205 | 2 | 23 |
| α-helix | 208-217 | 10 | |
| β-strand | 221 | 1 | 22 |
| β-strand | 222-227 | 6 | 23 |
| α-helix | 233-245 | 13 | |
| α-helix | 253-255 | 3 | |
| α-helix | 258-259 | 2 | |
| α-helix | 261-264 | 4 | |
| α-helix | 265-268 | 4 | |
| α-helix | 270-273 | 4 | |
Chain e: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-16 | 4 | |
| β-strand | 32-35 | 4 | 34 |
| β-strand | 45-47 | 3 | 34 |
| β-strand | 79-80 | 2 | 34 |
25 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 |
|---|
| rRNA | A | RNA | 1869 | Oryctolagus cuniculus | |
| eS25 | a | protein | 125 | Oryctolagus cuniculus | G1TDB3 (AlphaFold model) |
| 40S ribosomal protein SA | B | protein | 295 | Oryctolagus cuniculus | G1TLT8 (AlphaFold model) |
| 40S ribosomal protein S26 | b | protein | 115 | Oryctolagus cuniculus | G1TFE8 (AlphaFold model) |
| eS1 | C | protein | 264 | Oryctolagus cuniculus | G1SS70 (AlphaFold model) |
| uS5 | D | protein | 293 | Oryctolagus cuniculus | P15880 |
| eS28 | d | protein | 69 | Oryctolagus cuniculus | G1TIB4 |
| Ribosomal protein S3 | E | protein | 243 | Oryctolagus cuniculus | G1TNM3 |
| eS30 | f | protein | 133 | Oryctolagus cuniculus | G1T8A2 |
| uS7 | G | protein | 204 | Oryctolagus cuniculus | G1TFM5 |
| eS31 | g | protein | 156 | Oryctolagus cuniculus | P62979 |
| eS6 | H | protein | 249 | Oryctolagus cuniculus | A0A5K1UJS7 |
22 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>7JQB_1 rRNA (chains A)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA
Sequence of entity 2 (a), FASTA
>7JQB_2 eS25 (chains a)
MPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCK
EVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPA
AGEDA
Sequence of entity 3 (B), FASTA
>7JQB_3 40S ribosomal protein SA (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQTAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS
Sequence of entity 4 (b), FASTA
>7JQB_4 40S ribosomal protein S26 (chains b)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM
Sequence of entity 5 (C), FASTA
>7JQB_5 eS1 (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 6 (D), FASTA
>7JQB_6 uS5 (chains D)
MADDAGAAGGPGDPGGPGIGGRGGFRGGFGSGVRGRGRGRGRGRGRGRGARGGKAEDKEW
LPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
Sequence of entity 7 (d), FASTA
>7JQB_7 eS28 (chains d)
MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLE
SEREARRLR
Sequence of entity 8 (E), FASTA
>7JQB_8 Ribosomal protein S3 (chains E)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA
Sequence of entity 9 (f), FASTA
>7JQB_9 eS30 (chains f)
MQLFVRAQELHTLEVTGRETVAQIKAHVASLEGIAPEDQVVLLAGTPLEDEATLGQCGVE
ALSTLEVAGRMLGGKVHGSLARVGKVRGQTLKVAKQEKKKKRTGRAKRRMQYNRRFVNVV
PTFGKKKGPNANS
Sequence of entity 10 (G), FASTA
>7JQB_10 uS7 (chains G)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR
Sequence of entity 11 (g), FASTA
>7JQB_11 eS31 (chains g)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRE
CPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPEDK
Sequence of entity 12 (H), FASTA
>7JQB_12 eS6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK
Primary citation
Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Yuan, S., Peng, L., Park, J.J. et al. Mol Cell (2020) 80:1055-1066.e6. DOI 10.1016/j.molcel.2020.10.034 · PubMed
Other PDB entries of the same protein (UniProt G1TDB3 (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
- 11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
- 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…
- 8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
- 6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
- 7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
- 9BDL 2.8 Å, 80S ribosome with angiogenin
- 9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1
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