7TQL: Human 40S small ribosomal subunit
CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B. Determined by electron microscopy at 3.2 Å resolution. Released 27 Apr 2022.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organism
- Homo sapiens
- Chains
- 38
- Atoms
- 80,976
- Mol. weight
- 1234.82 kDa
- Ligands
- GNP, 5GP, ZN
- Released
- 27 Apr 2022
Explore 7TQL in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7TQL contains 230 α-helices and 285 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 1: 20 helices, 39 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 602-621 | 20 | |
| β-strand | 629 | 1 | 1 |
| α-helix | 630-632 | 3 | |
| β-strand | 633-637 | 5 | 2 |
| α-helix | 647-652 | 6 | |
| β-strand | 669-670 | 2 | 2 |
| α-helix | 676-685 | 10 | |
| β-strand | 699-702 | 4 | 2 |
| α-helix | 708-711 | 4 | |
| β-strand | 722-726 | 5 | 2 |
| α-helix | 729-731 | 3 | |
| α-helix | 735-746 | 12 | |
| β-strand | 751-755 | 5 | 2 |
| β-strand | 757 | 1 | 3 |
| α-helix | 772-777 | 6 | |
| α-helix | 781-799 | 19 | |
| β-strand | 805-806 | 2 | 4 |
| β-strand | 818-819 | 2 | 4 |
| β-strand | 820-822 | 3 | 2 |
| β-strand | 824 | 1 | 3 |
| α-helix | 831-844 | 14 | |
| β-strand | 851 | 1 | 1 |
| β-strand | 857-866 | 10 | 5 |
| β-strand | 870-879 | 10 | 5 |
| β-strand | 887-890 | 4 | 6 |
| α-helix | 891-892 | 2 | |
| β-strand | 897-900 | 4 | 6 |
| β-strand | 903-906 | 4 | 5 |
| α-helix | 907-908 | 2 | |
| β-strand | 920-922 | 3 | 5 |
| β-strand | 929-934 | 6 | 5 |
| β-strand | 945-947 | 3 | 5 |
| β-strand | 948-949 | 2 | 6 |
| β-strand | 981-985 | 5 | 7 |
| β-strand | 987 | 1 | 5 |
| α-helix | 988-1001 | 14 | |
| β-strand | 1005-1010 | 6 | 7 |
| β-strand | 1013 | 1 | 8 |
| α-helix | 1015-1025 | 11 | |
| β-strand | 1033-1037 | 5 | 7 |
| α-helix | 1040 | 1 | |
| β-strand | 1041 | 1 | 8 |
| α-helix | 1042 | 1 | |
| α-helix | 1043-1051 | 9 | |
| β-strand | 1055-1059 | 5 | 7 |
| α-helix | 1062-1081 | 20 | |
| β-strand | 1092-1096 | 5 | 9 |
| β-strand | 1103 | 1 | 9 |
| β-strand | 1108-1117 | 10 | 9 |
| β-strand | 1125-1129 | 5 | 9 |
| β-strand | 1131-1135 | 5 | 9 |
| β-strand | 1138-1143 | 6 | 9 |
| β-strand | 1146-1147 | 2 | 9 |
| β-strand | 1157-1161 | 5 | 9 |
| β-strand | 1172 | 1 | 10 |
| β-strand | 1176 | 1 | 10 |
| β-strand | 1182-1184 | 3 | 9 |
| α-helix | 1188-1195 | 8 | |
| α-helix | 1209-1214 | 6 | |
Chain 4: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 34-37 | 4 | 16 |
| β-strand | 49-51 | 3 | 16 |
| β-strand | 56-61 | 6 | 16 |
| α-helix | 63-65 | 3 | |
| β-strand | 76-80 | 5 | 16 |
| β-strand | 88-94 | 7 | 16 |
| α-helix | 97-106 | 10 | |
Chain a: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 47 | 1 | 17 |
| α-helix | 52-61 | 10 | |
| β-strand | 68 | 1 | 18 |
| α-helix | 70-77 | 8 | |
| β-strand | 79 | 1 | 17 |
| α-helix | 81-94 | 14 | |
| β-strand | 97-101 | 5 | 18 |
| β-strand | 108-111 | 4 | 18 |
Chain b: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 32-36 | 5 | 22 |
| β-strand | 44-47 | 4 | 22 |
| β-strand | 55-56 | 2 | 23 |
| β-strand | 61-62 | 2 | 23 |
| β-strand | 64-65 | 2 | 24 |
| α-helix | 71 | 1 | |
| β-strand | 72-73 | 2 | 24 |
| α-helix | 74 | 1 | |
| β-strand | 78-81 | 4 | 22 |
Chain B: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 19 |
| α-helix | 34-36 | 3 | |
| β-strand | 38-41 | 4 | 20 |
| β-strand | 47-49 | 3 | 20 |
| α-helix | 51-66 | 16 | |
| β-strand | 74-78 | 5 | 21 |
| α-helix | 84-94 | 11 | |
| β-strand | 97-100 | 4 | 21 |
| β-strand | 121-124 | 4 | 21 |
| α-helix | 131-136 | 6 | |
| α-helix | 137-139 | 3 | |
| β-strand | 144-148 | 5 | 21 |
| β-strand | 159-162 | 4 | 21 |
| α-helix | 168-186 | 19 | |
| α-helix | 194-195 | 2 | |
| α-helix | 199-202 | 4 | |
Chain c: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 28 |
| β-strand | 29-31 | 3 | 28 |
| β-strand | 36-43 | 8 | 29 |
| α-helix | 47-56 | 10 | |
| β-strand | 57 | 1 | 73 |
| α-helix | 63-65 | 3 | |
| β-strand | 66-73 | 8 | 29 |
| α-helix | 75-80 | 6 | |
| α-helix | 96-99 | 4 | |
Chain C: 10 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-27 | 4 | |
| β-strand | 28-34 | 7 | 25 |
| β-strand | 43-50 | 8 | 25 |
| α-helix | 58-61 | 4 | |
| β-strand | 66-69 | 4 | 25 |
| α-helix | 71-73 | 3 | |
| β-strand | 82-92 | 11 | 25 |
| β-strand | 95-105 | 11 | 25 |
| α-helix | 107-113 | 7 | |
| β-strand | 118 | 1 | 26 |
| β-strand | 120-128 | 9 | 25 |
| β-strand | 134-142 | 9 | 25 |
| β-strand | 143 | 1 | 27 |
| α-helix | 144-146 | 3 | |
| β-strand | 154 | 1 | 26 |
| α-helix | 158-177 | 20 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-200 | 9 | |
| β-strand | 207 | 1 | 27 |
| β-strand | 211-219 | 9 | 25 |
| α-helix | 221-223 | 3 | |
| α-helix | 225-232 | 8 | |
Chain d: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-19 | 10 | 33 |
| β-strand | 27-34 | 8 | 33 |
| β-strand | 41-47 | 7 | 33 |
| β-strand | 55-58 | 4 | 33 |
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 |
|---|
| Eukaryotic translation initiation factor 5B | 1 | protein | 619 | Homo sapiens | O60841 (AlphaFold model) |
| 18S ribosomal RNA | 2 | RNA | 1656 | Homo sapiens | |
| Human Met-tRNAiMet | 3 | RNA | 75 | Homo sapiens | |
| Translation initiation factor eIF1A | 4 | protein | 90 | Homo sapiens | P47813 (AlphaFold model) |
| ribosomal protein uS2 | B, C | protein | 419 | Homo sapiens | P08865 (AlphaFold model), P61247 (AlphaFold model) |
| 40S ribosomal protein S2 | D | protein | 218 | Homo sapiens | P15880 |
| 40S ribosomal protein S4, X isoform | E | protein | 258 | Homo sapiens | P62701 |
| 40S ribosomal protein S3 | F | protein | 225 | Homo sapiens | P23396 |
| 40S ribosomal protein S6 | G | protein | 226 | Homo sapiens | P62753 |
| 40S ribosomal protein S7 | H | protein | 185 | Homo sapiens | P62081 |
| 40S ribosomal protein S8 | I | protein | 205 | Homo sapiens | P62241 |
| 40S ribosomal protein S9 | J | protein | 180 | Homo sapiens | P46781 |
25 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>7TQL_1 Eukaryotic translation initiation factor 5B (chains 1)
EERAYDKAKRRIEKRRLEHSKNVTEKDKLRAPIICVLGHVDTGKTKILDKLRHTHVQDGE
AGGITQQIGATNVPLEAINEQTKMIKNFDRENVRIPGMLIIDTPGHESFSNLRNRGSSLC
DIAILVVDIMHGLEPQTIESINLLKSKKCPFIVALNKIDRLYDWKKSPDSDVAATLKKQK
KNTKDEFEERAKAIIVEFAQQGLNAALFYENKDPRTFVSLVPTSAHTGDGMGSLIYLLVE
LTQTMLSKRLAHCEELRAQVMEVKALPGMGTTIDVILINGRLKEGDTIIVPGVEGPIVTQ
IRGLLTPPPMKELRVKNQYEKHKEVEAAQGVKILGKDLEKTLAGLPLLVAYKEDEIPVLK
DELIHELKQTLNAIKLEEKGVYVQASTLGSLEALLEFLKTSEVPYAGINIGPVHKKDVMK
ASVMLEHDPQYAVILAFDVRIERDAQEMADSLGVRIFSAEIIYHLFDAFTKYRQDYKKQK
QEEFKHIAVFPCKIKILPQYIFNSRDPIVMGVTVEAGQVKQGTPMCVPSKNFVDIGIVTS
IEINHKQVDVAKKGQEVCVKIEPIPGESPKMFGRHFEATDILVSKISRQSIDALKDWFRD
EMQKSDWQLIVELKKVFEI
Sequence of entity 2 (2), FASTA
>7TQL_2 18S ribosomal RNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCU
GACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGUGGUGACUCUAGAUAACCUCGGGC
CGAUCGCACGCCGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUA
GUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAG
GGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUC
CCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAU
UGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCA
GCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUC
GUAGUUGGAUCUCUAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCGCCUGG
AUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACU
GAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUU
CUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUC
AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACG
AUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAAC
CAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACG
GAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCAC
CCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGU
GGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGA
GACUCUGGCAUGCUAACUAGUUACGCGACCGGUCGGCGUAACUUCUUAGAGGGACAAGUG
GCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGC
UGCACGCGCGCUACACUGACUGGCUCAGCGUGUCCUACGCCGGCAGGCGCGGGUAACCCG
UUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUC
CCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCC
CGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUGCC
CUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAAC
AAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 3 (3), FASTA
>7TQL_3 Human Met-tRNAiMet (chains 3)
AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAAC
CAUCCUCUGCUACCA
Sequence of entity 4 (4), FASTA
>7TQL_4 Translation initiation factor eIF1A (chains 4)
RELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRD
YQDNKADVILKYNADEARSLKAYGELPEHA
Sequence of entity 5 (B, C), FASTA
>7TQL_5 ribosomal protein uS2 (chains B, C)
SGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLA
ARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRL
LVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLARE
VLRMRGTISREHPWEVMPDLYFYRDPVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQG
TKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMV
KKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTR
EVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHG
Sequence of entity 6 (D), FASTA
>7TQL_6 40S ribosomal protein S2 (chains D)
EWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRA
GQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPH
TVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAK
ATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKT
Sequence of entity 7 (E), FASTA
>7TQL_7 40S ribosomal protein S4, X isoform (chains E)
ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEV
KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKY
KLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLC
MVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG
KGIRLTIAEERDKRLAAK
Sequence of entity 8 (F), FASTA
>7TQL_8 40S ribosomal protein S3 (chains F)
VQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEK
GRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGV
LRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVL
GIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK
Sequence of entity 9 (G), FASTA
>7TQL_9 40S ribosomal protein S6 (chains G)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQE
Sequence of entity 10 (H), FASTA
>7TQL_10 40S ribosomal protein S7 (chains H)
IVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVP
QLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHD
AILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNF
EFPEF
Sequence of entity 11 (I), FASTA
>7TQL_11 40S ribosomal protein S8 (chains I)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARK
Sequence of entity 12 (J), FASTA
>7TQL_12 40S ribosomal protein S9 (chains J)
PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELL
TLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAK
SIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GNP | Phosphoaminophosphonic acid-guanylate ester | C10 H17 N6 O13 P3 | 1 |
| 5GP | Guanosine-5'-monophosphate | C10 H14 N5 O8 P | 1 |
| ZN | Zinc ion | Zn | 3 |
Primary citation
eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining. Lapointe, C.P., Grosely, R., Sokabe, M. et al. Nature (2022) 607:185-190. DOI 10.1038/s41586-022-04858-z · PubMed
Other PDB entries of the same protein (UniProt O60841 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
- 8PJ4 3.2 Å, Structure of human 48S translation initiation complex after eIF5 release (48S-4)
- 9KRP 3.2 Å, Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3
- 9KN6 3.3 Å, Structure of the HCV IRES-dependent pre-48S translation initiation complex with eIF1A,…
- 8PJ3 3.7 Å, Structure of human 48S translation initiation complex upon transfer of initiator tRNA to…
Browse structure collections
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