4D61: 40S ribosomal protein sa
Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state. Determined by electron microscopy at 9.0 Å resolution. Released 4 Mar 2015.
- Method
- Electron microscopy
- Resolution
- 9.0 Å
- Organisms
- ORYCTOLAGUS CUNICULUS, HOMO SAPIENS, CRICKET PARALYSIS VIRUS
- Chains
- 37
- Atoms
- 86,384
- Mol. weight
- 1383.14 kDa
- Released
- 4 Mar 2015
Explore 4D61 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4D61 contains 240 α-helices and 277 β-strands across 35 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: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 6 |
| β-strand | 29-31 | 3 | 6 |
| β-strand | 36 | 1 | 7 |
| β-strand | 40-43 | 4 | 8 |
| α-helix | 47-55 | 9 | |
| β-strand | 66-69 | 4 | 8 |
| β-strand | 73 | 1 | 7 |
| α-helix | 75-78 | 4 | |
Chain A: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 3 |
| β-strand | 38-41 | 4 | 4 |
| α-helix | 42 | 1 | |
| β-strand | 47-49 | 3 | 4 |
| α-helix | 51-65 | 15 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 5 |
| α-helix | 81-93 | 13 | |
| β-strand | 97-100 | 4 | 5 |
| β-strand | 121-124 | 4 | 5 |
| α-helix | 131-140 | 10 | |
| β-strand | 144-148 | 5 | 5 |
| β-strand | 159-162 | 4 | 5 |
| α-helix | 168-186 | 19 | |
| α-helix | 194-195 | 2 | |
| α-helix | 199-201 | 3 | |
| α-helix | 206-218 | 13 | |
Chain b: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| α-helix | 20-22 | 3 | |
| β-strand | 32-36 | 5 | 12 |
| β-strand | 43-47 | 5 | 12 |
| β-strand | 54-55 | 2 | 13 |
| β-strand | 62-65 | 4 | 13 |
| α-helix | 71 | 1 | |
| β-strand | 72-73 | 2 | 13 |
| β-strand | 79-81 | 3 | 12 |
Chain B: 9 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-32 | 3 | 9 |
| β-strand | 33 | 1 | 10 |
| β-strand | 34 | 1 | 9 |
| α-helix | 35-36 | 2 | |
| β-strand | 43-48 | 6 | 9 |
| α-helix | 58-62 | 5 | |
| β-strand | 66-70 | 5 | 11 |
| α-helix | 71-75 | 5 | |
| β-strand | 83-87 | 5 | 11 |
| β-strand | 91-92 | 2 | 10 |
| β-strand | 95-96 | 2 | 10 |
| β-strand | 99-104 | 6 | 11 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-128 | 9 | 11 |
| β-strand | 134-142 | 9 | 11 |
| α-helix | 159-175 | 17 | |
| α-helix | 180-188 | 9 | |
| α-helix | 192-201 | 10 | |
| β-strand | 208-211 | 4 | 11 |
| β-strand | 215-219 | 5 | 11 |
| α-helix | 225-228 | 4 | |
| α-helix | 229-231 | 3 | |
Chain c: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-21 | 13 | 18 |
| β-strand | 27-34 | 8 | 18 |
| β-strand | 41-47 | 7 | 18 |
| β-strand | 55-59 | 5 | 18 |
Chain C: 13 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-71 | 7 | |
| α-helix | 78-84 | 7 | |
| α-helix | 92-97 | 6 | |
| α-helix | 99-102 | 4 | |
| β-strand | 104-115 | 12 | 14 |
| β-strand | 120-130 | 11 | 14 |
| β-strand | 136-137 | 2 | 15 |
| β-strand | 138-144 | 7 | 14 |
| α-helix | 147-160 | 14 | |
| β-strand | 163-164 | 2 | 15 |
| β-strand | 168 | 1 | 16 |
| β-strand | 179 | 1 | 16 |
| β-strand | 184-188 | 5 | 17 |
| β-strand | 191-196 | 6 | 17 |
| β-strand | 204-205 | 2 | 17 |
| α-helix | 208-217 | 10 | |
| β-strand | 222-227 | 6 | 17 |
| α-helix | 233-246 | 14 | |
| α-helix | 247-249 | 3 | |
| α-helix | 253-255 | 3 | |
| α-helix | 258-259 | 2 | |
| α-helix | 262-264 | 3 | |
| α-helix | 265-268 | 4 | |
| α-helix | 270-273 | 4 | |
Chain d: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| α-helix | 30 | 1 | |
| β-strand | 31 | 1 | 22 |
| α-helix | 32 | 1 | |
| β-strand | 39 | 1 | 22 |
| α-helix | 40-50 | 11 | |
Chain D: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| β-strand | 34-41 | 8 | 19 |
| β-strand | 46-52 | 7 | 19 |
| α-helix | 55-59 | 5 | |
| α-helix | 64-77 | 14 | |
| β-strand | 84-90 | 7 | 19 |
| α-helix | 91 | 1 | |
| α-helix | 98-110 | 13 | |
| α-helix | 115-129 | 15 | |
| β-strand | 133-140 | 8 | 20 |
| β-strand | 148-155 | 8 | 20 |
| α-helix | 164-167 | 4 | |
| β-strand | 168-176 | 9 | 20 |
| β-strand | 181-189 | 9 | 20 |
| α-helix | 190-192 | 3 | |
| α-helix | 203-204 | 2 | |
| β-strand | 209-210 | 2 | 21 |
27 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 | 1 | RNA | 1869 | ORYCTOLAGUS CUNICULUS | |
| 40S ribosomal protein sa | A | protein | 295 | ORYCTOLAGUS CUNICULUS | G1TLT8 (AlphaFold model) |
| 40S ribosomal protein S3A | B | protein | 264 | ORYCTOLAGUS CUNICULUS | G1SS70 (AlphaFold model) |
| 40S ribosomal protein S2 | C | protein | 293 | ORYCTOLAGUS CUNICULUS | G1SWM1 (AlphaFold model) |
| 40S ribosomal protein S3 | D | protein | 243 | ORYCTOLAGUS CUNICULUS | G1TNM3 (AlphaFold model) |
| 40S ribosomal protein S4, Y isoform 1 | E | protein | 263 | ORYCTOLAGUS CUNICULUS | G1TK17 |
| 40S ribosomal protein S5 | F | protein | 204 | ORYCTOLAGUS CUNICULUS | G1TFM5 |
| 40S ribosomal protein S6 | G | protein | 249 | ORYCTOLAGUS CUNICULUS | G1TM55 |
| 40S ribosomal protein S7 | H | protein | 194 | ORYCTOLAGUS CUNICULUS | G1SVB0 |
| 40S ribosomal protein S8 | I | protein | 208 | ORYCTOLAGUS CUNICULUS | G1TJW1 |
| 40S ribosomal protein S9 | J | protein | 194 | ORYCTOLAGUS CUNICULUS | B7NZS8 |
| 40S ribosomal protein S10 | K | protein | 165 | ORYCTOLAGUS CUNICULUS | G1T168 |
25 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>4D61_1 18S RRNA (chains 1)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
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
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCUCGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA
Sequence of entity 2 (A), FASTA
>4D61_2 40S RIBOSOMAL PROTEIN SA (chains A)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS
Sequence of entity 3 (B), FASTA
>4D61_3 40S RIBOSOMAL PROTEIN S3A (chains B)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 4 (C), FASTA
>4D61_4 40S RIBOSOMAL PROTEIN S2 (chains C)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
Sequence of entity 5 (D), FASTA
>4D61_5 40S RIBOSOMAL PROTEIN S3 (chains D)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA
Sequence of entity 6 (E), FASTA
>4D61_6 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1 (chains E)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRVDVTYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAK
YKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTVQIDLGTGKIINFIKFDTGNL
CMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGNGNKPWISLPR
GKGIRLTVAEERDKRLATKQSSG
Sequence of entity 7 (F), FASTA
>4D61_7 40S RIBOSOMAL PROTEIN S5 (chains F)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR
Sequence of entity 8 (G), FASTA
>4D61_8 40S RIBOSOMAL PROTEIN S6 (chains G)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK
Sequence of entity 9 (H), FASTA
>4D61_9 40S RIBOSOMAL PROTEIN S7 (chains H)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL
Sequence of entity 10 (I), FASTA
>4D61_10 40S RIBOSOMAL PROTEIN S8 (chains I)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK
Sequence of entity 11 (J), FASTA
>4D61_11 40S RIBOSOMAL PROTEIN S9 (chains J)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED
Sequence of entity 12 (K), FASTA
>4D61_12 40S RIBOSOMAL PROTEIN S10 (chains K)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ
Primary citation
Cryo-Em of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus Ires. Muhs, M., Hilal, T., Mielke, T. et al. Mol Cell (2015) 57:422. DOI 10.1016/J.MOLCEL.2014.12.016 · 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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