7SYR: PDB entry 7SYR
Structure of the wt IRES eIF2-containing 48S initiation complex, closed conformation. Structure 12(wt). Determined by electron microscopy at 3.6 Å resolution. Released 27 Jul 2022.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organisms
- Oryctolagus cuniculus, Homo sapiens, Hepatitis C virus (isolate 1)
- Chains
- 39
- Atoms
- 83,005
- Mol. weight
- 1466.6 kDa
- Ligands
- ZN
- Released
- 27 Jul 2022
Explore 7SYR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7SYR contains 204 α-helices and 261 β-strands across 36 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, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 47 | 1 | 3 |
| β-strand | 50 | 1 | 68 |
| α-helix | 52-61 | 10 | |
| α-helix | 62-64 | 3 | |
| β-strand | 67-68 | 2 | 4 |
| α-helix | 70-77 | 8 | |
| β-strand | 79 | 1 | 3 |
| α-helix | 81-94 | 14 | |
| β-strand | 98-101 | 4 | 4 |
| β-strand | 108-110 | 3 | 4 |
| α-helix | 111-113 | 3 | |
Chain A: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 33-38 | 6 | 2 |
| β-strand | 46-51 | 6 | 2 |
| β-strand | 56-60 | 5 | 2 |
| β-strand | 76-80 | 5 | 2 |
| β-strand | 88 | 1 | 2 |
| β-strand | 94-95 | 2 | 2 |
| α-helix | 98-106 | 9 | |
Chain b: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 8 |
| β-strand | 29-31 | 3 | 8 |
| β-strand | 36-43 | 8 | 9 |
| α-helix | 50-54 | 5 | |
| β-strand | 57 | 1 | 61 |
| α-helix | 63-65 | 3 | |
| β-strand | 66-73 | 8 | 9 |
| α-helix | 75-80 | 6 | |
| α-helix | 97-99 | 3 | |
Chain B: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-20 | 7 | |
| β-strand | 25 | 1 | 5 |
| α-helix | 32-37 | 6 | |
| β-strand | 38-42 | 5 | 6 |
| β-strand | 46-49 | 4 | 6 |
| α-helix | 51-67 | 17 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 7 |
| α-helix | 81-83 | 3 | |
| α-helix | 84-94 | 11 | |
| β-strand | 97-100 | 4 | 7 |
| β-strand | 121-124 | 4 | 7 |
| α-helix | 131-136 | 6 | |
| β-strand | 144-148 | 5 | 7 |
| β-strand | 159-162 | 4 | 7 |
| α-helix | 168-186 | 19 | |
| α-helix | 199-202 | 4 | |
| α-helix | 207-216 | 10 | |
Chain c: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 32-34 | 3 | 14 |
| β-strand | 45-47 | 3 | 14 |
| β-strand | 55 | 1 | 15 |
| β-strand | 62 | 1 | 15 |
| β-strand | 64-65 | 2 | 16 |
| β-strand | 72-73 | 2 | 16 |
| β-strand | 80 | 1 | 14 |
Chain C: 10 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-27 | 4 | |
| β-strand | 28-30 | 3 | 10 |
| β-strand | 33-34 | 2 | 11 |
| β-strand | 43-45 | 3 | 11 |
| β-strand | 48-50 | 3 | 10 |
| α-helix | 51-52 | 2 | |
| β-strand | 53 | 1 | 12 |
| β-strand | 56 | 1 | 12 |
| α-helix | 58-61 | 4 | |
| β-strand | 66-70 | 5 | 11 |
| β-strand | 82-91 | 10 | 11 |
| β-strand | 96-105 | 10 | 11 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-125 | 6 | 11 |
| β-strand | 128 | 1 | 13 |
| β-strand | 134 | 1 | 13 |
| β-strand | 137-143 | 7 | 11 |
| α-helix | 144-146 | 3 | |
| α-helix | 158-177 | 20 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-200 | 9 | |
| α-helix | 201-203 | 3 | |
| β-strand | 207-215 | 9 | 11 |
| β-strand | 219 | 1 | 13 |
| α-helix | 225-230 | 6 | |
Chain d: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| β-strand | 10-17 | 8 | 20 |
| β-strand | 27-34 | 8 | 20 |
| β-strand | 41-47 | 7 | 20 |
| β-strand | 55-58 | 4 | 20 |
Chain D: 11 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-71 | 7 | |
| α-helix | 79-83 | 5 | |
| α-helix | 92-97 | 6 | |
| β-strand | 103-115 | 13 | 17 |
| β-strand | 120-131 | 12 | 17 |
| β-strand | 137-144 | 8 | 17 |
| α-helix | 147-160 | 14 | |
| β-strand | 162-163 | 2 | 17 |
| β-strand | 168 | 1 | 18 |
| β-strand | 179 | 1 | 18 |
| β-strand | 184-188 | 5 | 19 |
| β-strand | 191-196 | 6 | 19 |
| β-strand | 204-205 | 2 | 19 |
| α-helix | 208-217 | 10 | |
| β-strand | 221 | 1 | 18 |
| β-strand | 222-227 | 6 | 19 |
| α-helix | 233-245 | 13 | |
| α-helix | 253-255 | 3 | |
| α-helix | 258-260 | 3 | |
| α-helix | 262-264 | 3 | |
| α-helix | 265-268 | 4 | |
| α-helix | 270-276 | 7 | |
28 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 | |
| Eukaryotic translation initiation factor 1A, X-chromosomal | A | protein | 144 | Homo sapiens | P47813 (AlphaFold model) |
| uS2 (SA) | B | protein | 295 | Oryctolagus cuniculus | G1TLT8 (AlphaFold model) |
| eS1 | C | protein | 264 | Oryctolagus cuniculus | G1SS70 (AlphaFold model) |
| uS5 | D | protein | 221 | Oryctolagus cuniculus | G1SV32 (AlphaFold model) |
| uS3 | E | protein | 281 | Oryctolagus cuniculus | G1TNM3 |
| eS4 (S4 X isoform) | F | protein | 263 | Oryctolagus cuniculus | G1TA47 |
| uS7 | G | protein | 204 | Oryctolagus cuniculus | G1TFM5 |
| eS6 | H | protein | 249 | Oryctolagus cuniculus | A0A5K1UJS7 |
| eS7 | I | protein | 432 | Oryctolagus cuniculus | G1SVB0 |
| eS8 | J | protein | 208 | Oryctolagus cuniculus | G1TJW1 |
| uS4 | K | protein | 194 | Oryctolagus cuniculus | B7NZS8 |
27 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>7SYR_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 (A), FASTA
>7SYR_2 Eukaryotic translation initiation factor 1A, X-chromosomal (chains A)
MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCH
IRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDT
FGPGDDDEIQFDDIGDDDEDIDDI
Sequence of entity 3 (B), FASTA
>7SYR_3 uS2 (SA) (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQTAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS
Sequence of entity 4 (C), FASTA
>7SYR_4 eS1 (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 5 (D), FASTA
>7SYR_5 uS5 (chains D)
KEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTR
AGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKP
HTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFA
KATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT
Sequence of entity 6 (E), FASTA
>7SYR_6 uS3 (chains E)
MSARRRRRRAAFRRRAEPFIPISVREPLPFLSAARGGKMAVQISKKRKFVADGIFKAELN
EFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG
SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKL
RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKK
PLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA
Sequence of entity 7 (F), FASTA
>7SYR_7 eS4 (S4 X isoform) (chains F)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG
Sequence of entity 8 (G), FASTA
>7SYR_8 uS7 (chains G)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR
Sequence of entity 9 (H), FASTA
>7SYR_9 eS6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK
Sequence of entity 10 (I), FASTA
>7SYR_10 eS7 (chains I)
EPITNRVFQALTSSDFKQQDGGSFSLSRTHLSGFRSRPRRTTIASAATRPPPIPSRGGSA
PTGTPEGAGASRSSRTVPRLPPQPSGPPRAPRHPGFQRALPSLIRPEPGVRAPLLASAGT
RFKRPASQAVKALSARGLLQPQVQVGPRANRVPQRREPRQHLSGHAPGASEGGSASPTYW
SLGITSWDALGFPLRLGGSSGFRSSVALFRPLSFRRGDLPRSREIWASSSAGAQPGEAMF
SSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIII
FVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTL
TAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTG
KDVNFEFPEFQL
Sequence of entity 11 (J), FASTA
>7SYR_11 eS8 (chains J)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK
Sequence of entity 12 (K), FASTA
>7SYR_12 uS4 (chains K)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. Brown, Z.P., Abaeva, I.S., De, S. et al. EMBO J (2022) 41:e110581-e110581. DOI 10.15252/embj.2022110581 · PubMed
Other PDB entries of the same protein (UniProt P47813 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 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)
- 28ZV 2.9 Å, human 48S PIC with mRNA (non-Kozak)
- 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…
- 9H74 2.9 Å, Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA
- 28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
- 6YBW 3.1 Å, Structure of a human 48S translational initiation complex - 40S body
- 8SUP 3.1 Å, Structure of the 48S translation initiation complex assembled on the…
- 28ZU 3.2 Å, human 48S PIC with Kozak mRNA and eIF1A W70A mutant
- 7TQL 3.2 Å, CryoEM structure of the human 40S small ribosomal subunit in complex with translation…
Browse structure collections
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