8XXM: Human 40S ribosome with PDCD4 and eIF3G
Cryo-EM structure of the human 40S ribosome with PDCD4 and eIF3G. Determined by electron microscopy at 3.2 Å resolution. Released 1 May 2024.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organism
- Homo sapiens
- Chains
- 37
- Atoms
- 76,934
- Mol. weight
- 1313.68 kDa
- Ligands
- ZN, MG
- Released
- 1 May 2024
Explore 8XXM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8XXM contains 200 α-helices and 240 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 3G: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 240-244 | 5 | 37 |
| α-helix | 252-259 | 8 | |
| β-strand | 265-272 | 8 | 37 |
| β-strand | 279-287 | 9 | 37 |
| α-helix | 290-300 | 11 | |
| β-strand | 304 | 1 | 11 |
| β-strand | 309 | 1 | 11 |
| β-strand | 311-314 | 4 | 37 |
| α-helix | 315-317 | 3 | |
Chain CD: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 112-113 | 2 | |
| α-helix | 114-117 | 4 | |
| α-helix | 131-137 | 7 | |
Chain Ln: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-23 | 21 | |
Chain Sa: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 52 |
| β-strand | 28 | 1 | 53 |
| β-strand | 29-31 | 3 | 52 |
| β-strand | 36-43 | 8 | 54 |
| α-helix | 47-49 | 3 | |
| α-helix | 51-56 | 6 | |
| β-strand | 57 | 1 | 4 |
| α-helix | 63-65 | 3 | |
| β-strand | 66-73 | 8 | 54 |
| α-helix | 75-80 | 6 | |
| α-helix | 96-99 | 4 | |
Chain SA: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 2 |
| α-helix | 35-37 | 3 | |
| β-strand | 38-41 | 4 | 2 |
| β-strand | 47-49 | 3 | 2 |
| α-helix | 51-66 | 16 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 3 |
| α-helix | 81-93 | 13 | |
| β-strand | 97-100 | 4 | 3 |
| β-strand | 121-124 | 4 | 3 |
| α-helix | 131-139 | 9 | |
| β-strand | 144-148 | 5 | 3 |
| β-strand | 159-162 | 4 | 3 |
| α-helix | 168-186 | 19 | |
| α-helix | 194-195 | 2 | |
| α-helix | 199-201 | 3 | |
| α-helix | 207-222 | 16 | |
Chain Sb: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 32-35 | 4 | 25 |
| β-strand | 44-47 | 4 | 25 |
| β-strand | 54-55 | 2 | 26 |
| β-strand | 62-65 | 4 | 26 |
| α-helix | 71 | 1 | |
| β-strand | 72-73 | 2 | 26 |
| β-strand | 80-81 | 2 | 25 |
Chain SB: 8 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 28-34 | 7 | 5 |
| β-strand | 43-50 | 8 | 5 |
| α-helix | 58-62 | 5 | |
| β-strand | 65-66 | 2 | 5 |
| β-strand | 69-70 | 2 | 6 |
| β-strand | 82-84 | 3 | 6 |
| β-strand | 87-92 | 6 | 5 |
| β-strand | 95-99 | 5 | 5 |
| β-strand | 102-105 | 4 | 6 |
| α-helix | 107-113 | 7 | |
| β-strand | 118 | 1 | 7 |
| β-strand | 120-128 | 9 | 6 |
| β-strand | 134-142 | 9 | 6 |
| β-strand | 143 | 1 | 8 |
| β-strand | 154 | 1 | 7 |
| α-helix | 155-157 | 3 | |
| α-helix | 158-178 | 21 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-200 | 9 | |
| α-helix | 201-203 | 3 | |
| β-strand | 207 | 1 | 8 |
| β-strand | 211-219 | 9 | 6 |
| α-helix | 225-232 | 8 | |
Chain Sc: 0 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-13 | 4 | 55 |
| β-strand | 14 | 1 | 56 |
| β-strand | 21 | 1 | 24 |
| β-strand | 27-29 | 3 | 24 |
| β-strand | 32 | 1 | 56 |
| β-strand | 45-47 | 3 | 24 |
| β-strand | 55-58 | 4 | 55 |
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 |
|---|
| 60S ribosomal protein L41 | Ln | protein | 25 | Homo sapiens | P62945 (AlphaFold model) |
| 18S rRNA | S2 | RNA | 1869 | Homo sapiens | |
| 40S ribosomal protein SA | SA | protein | 295 | Homo sapiens | P08865 (AlphaFold model) |
| 40S ribosomal protein S3a | SB | protein | 264 | Homo sapiens | P61247 (AlphaFold model) |
| 40S ribosomal protein S3 | SD | protein | 243 | Homo sapiens | P23396 (AlphaFold model) |
| 40S ribosomal protein S4, X isoform | SE | protein | 263 | Homo sapiens | P62701 |
| 40S ribosomal protein S5 | SF | protein | 204 | Homo sapiens | P46782 |
| 40S ribosomal protein S7 | SH | protein | 194 | Homo sapiens | P62081 |
| 40S ribosomal protein S8 | SI | protein | 208 | Homo sapiens | P62241 |
| 40S ribosomal protein S10 | SK | protein | 165 | Homo sapiens | P46783 |
| 40S ribosomal protein S11 | SL | protein | 158 | Homo sapiens | P62280 |
| 40S ribosomal protein S15 | SP | protein | 145 | Homo sapiens | P62841 |
25 more molecules are not listed.
Sequence of entity 1 (Ln), FASTA
>8XXM_1 60S ribosomal protein L41 (chains Ln)
MRAKWRKKRMRRLKRKRRKMRQRSK
Sequence of entity 2 (S2), FASTA
>8XXM_2 18S rRNA (chains S2)
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
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA
Sequence of entity 3 (SA), FASTA
>8XXM_3 40S ribosomal protein SA (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS
Sequence of entity 4 (SB), FASTA
>8XXM_4 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 5 (SD), FASTA
>8XXM_5 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA
Sequence of entity 6 (SE), FASTA
>8XXM_6 40S ribosomal protein S4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG
Sequence of entity 7 (SF), FASTA
>8XXM_7 40S ribosomal protein S5 (chains SF)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR
Sequence of entity 8 (SH), FASTA
>8XXM_8 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL
Sequence of entity 9 (SI), FASTA
>8XXM_9 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK
Sequence of entity 10 (SK), FASTA
>8XXM_10 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ
Sequence of entity 11 (SL), FASTA
>8XXM_11 40S ribosomal protein S11 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF
Sequence of entity 12 (SP), FASTA
>8XXM_12 40S ribosomal protein S15 (chains SP)
MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRL
RKAKKEAPPMEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFS
ITYKPVKHGRPGIGATHSSRFIPLK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
| MG | Magnesium ion | Mg | 23 |
Primary citation
Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation. Ye, X., Huang, Z., Li, Y. et al. Cell Res (2024) 34:522-525. DOI 10.1038/s41422-024-00962-z · PubMed
Other PDB entries of the same protein (UniProt P62945 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
- 8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
- 9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
- 8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
- 9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
- 29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
- 9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
- 7R4X 2.15 Å, Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map
- 9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
- 9PBE 2.19 Å, In situ human 80S ribosome (composite map)
- 8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline
- 9O3V 2.2 Å, Human 80S ribosome stalled on MYC nascent chain
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