6YBW: 40S ribosomal protein S4, X isoform
Structure of a human 48S translational initiation complex - 40S body. Determined by electron microscopy at 3.1 Å resolution. Released 16 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Homo sapiens
- Chains
- 26
- Atoms
- 52,840
- Mol. weight
- 1154.85 kDa
- Ligands
- ZN, MG
- Released
- 16 Sept 2020
Explore 6YBW in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6YBW contains 140 α-helices and 146 β-strands across 24 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 9: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-22 | 20 | |
Chain B: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-47 | 3 | |
| β-strand | 72-79 | 8 | 8 |
| β-strand | 85-96 | 12 | 8 |
| β-strand | 101-112 | 12 | 8 |
| β-strand | 125-130 | 6 | 8 |
| β-strand | 140-146 | 7 | 8 |
Chain C: 9 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10 | 1 | 1 |
| α-helix | 11-13 | 3 | |
| α-helix | 16-18 | 3 | |
| β-strand | 27 | 1 | 1 |
| α-helix | 31-32 | 2 | |
| β-strand | 42-43 | 2 | 2 |
| α-helix | 44-50 | 7 | |
| α-helix | 60-65 | 6 | |
| β-strand | 70-72 | 3 | 3 |
| β-strand | 75-76 | 2 | 3 |
| β-strand | 83-84 | 2 | 2 |
| β-strand | 89-92 | 4 | 3 |
| β-strand | 97-100 | 4 | 3 |
| β-strand | 103 | 1 | 4 |
| β-strand | 109 | 1 | 4 |
| β-strand | 113 | 1 | 3 |
| α-helix | 118-120 | 3 | |
| β-strand | 121-125 | 5 | 5 |
| β-strand | 126-132 | 7 | 6 |
| β-strand | 136-141 | 6 | 6 |
| β-strand | 146-148 | 3 | 6 |
| β-strand | 159-163 | 5 | 5 |
| β-strand | 169-173 | 5 | 5 |
| β-strand | 180-183 | 4 | 7 |
| β-strand | 192-199 | 8 | 7 |
| β-strand | 207-211 | 5 | 7 |
| β-strand | 217-221 | 5 | 7 |
| α-helix | 222-224 | 3 | |
| β-strand | 225-230 | 6 | 7 |
| β-strand | 233-234 | 2 | 7 |
| α-helix | 237-239 | 3 | |
| α-helix | 248-255 | 8 | |
Chain D: 9 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-35 | 14 | |
| α-helix | 41-62 | 22 | |
| α-helix | 64 | 1 | |
| α-helix | 68-84 | 17 | |
| α-helix | 94-97 | 4 | |
| β-strand | 109 | 1 | 10 |
| α-helix | 110-115 | 6 | |
| α-helix | 123-131 | 9 | |
| β-strand | 135-137 | 3 | 11 |
| β-strand | 140-141 | 2 | 11 |
| β-strand | 148 | 1 | 10 |
| α-helix | 154-156 | 3 | |
| β-strand | 157-159 | 3 | 11 |
| α-helix | 172-175 | 4 | |
Chain E: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-20 | 11 | |
| α-helix | 25-31 | 7 | |
| β-strand | 46-58 | 13 | 9 |
| β-strand | 66-74 | 9 | 9 |
| β-strand | 80-84 | 5 | 9 |
| α-helix | 90-93 | 4 | |
| β-strand | 99-104 | 6 | 9 |
| β-strand | 120-125 | 6 | 9 |
| β-strand | 128-129 | 2 | 9 |
| α-helix | 130-134 | 5 | |
Chain F: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-15 | 5 | |
| α-helix | 24-28 | 5 | |
| α-helix | 31-42 | 12 | |
Chain G: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-32 | 15 | |
| β-strand | 47-53 | 7 | 12 |
| β-strand | 57-64 | 8 | 12 |
| α-helix | 66-68 | 3 | |
| α-helix | 69-72 | 4 | |
| α-helix | 76-86 | 11 | |
| β-strand | 90-96 | 7 | 12 |
| α-helix | 101-104 | 4 | |
| α-helix | 115-117 | 3 | |
| α-helix | 118-120 | 3 | |
| α-helix | 122-133 | 12 | |
| β-strand | 139-146 | 8 | 13 |
| β-strand | 152-158 | 7 | 13 |
| α-helix | 163-166 | 4 | |
| α-helix | 170-181 | 12 | |
| β-strand | 185-188 | 4 | 13 |
Chain H: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 32-36 | 5 | 14 |
| β-strand | 44-47 | 4 | 14 |
| β-strand | 54-55 | 2 | 15 |
| α-helix | 56 | 1 | |
| β-strand | 62-65 | 4 | 15 |
| β-strand | 72-73 | 2 | 15 |
| α-helix | 74 | 1 | |
| β-strand | 78-81 | 4 | 14 |
16 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 |
|---|
| 40S ribosomal protein S4, X isoform | C | protein | 263 | Homo sapiens | P62701 (AlphaFold model) |
| 40S ribosomal protein S11 | B | protein | 157 | Homo sapiens | P62280 (AlphaFold model) |
| 40S ribosomal protein S23 | E | protein | 143 | Homo sapiens | P62266 (AlphaFold model) |
| 40S ribosomal protein S9 | D | protein | 194 | Homo sapiens | P46781 (AlphaFold model) |
| 40S ribosomal protein S7 | G | protein | 194 | Homo sapiens | P62081 |
| 40S ribosomal protein S30 | F | protein | 59 | Homo sapiens | P62861 |
| 40S ribosomal protein S27 | H | protein | 84 | Homo sapiens | P42677 |
| 40S ribosomal protein S21 | K | protein | 83 | Homo sapiens | P63220 |
| 40S ribosomal protein S15a | J | protein | 130 | Homo sapiens | P62244 |
| 40S ribosomal protein S17 | M | protein | 135 | Homo sapiens | P08708 |
| 40S ribosomal protein S2 | L | protein | 293 | Homo sapiens | P15880 |
| 40S ribosomal protein S3a | O | protein | 264 | Homo sapiens | P61247 |
14 more molecules are not listed.
Sequence of entity 1 (C), FASTA
>6YBW_1 40S ribosomal protein S4, X isoform (chains C)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG
Sequence of entity 2 (B), FASTA
>6YBW_2 40S ribosomal protein S11 (chains B)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQK
Sequence of entity 3 (E), FASTA
>6YBW_3 40S ribosomal protein S23 (chains E)
MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAK
QPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRF
KVVKVANVSLLALYKGKKERPRS
Sequence of entity 4 (D), FASTA
>6YBW_4 40S ribosomal protein S9 (chains D)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED
Sequence of entity 5 (G), FASTA
>6YBW_5 40S ribosomal protein S7 (chains G)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL
Sequence of entity 6 (F), FASTA
>6YBW_6 40S ribosomal protein S30 (chains F)
KVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS
Sequence of entity 7 (H), FASTA
>6YBW_7 40S ribosomal protein S27 (chains H)
MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS
TVLCQPTGGKARLTEGCSFRRKQH
Sequence of entity 8 (K), FASTA
>6YBW_8 40S ribosomal protein S21 (chains K)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF
Sequence of entity 9 (J), FASTA
>6YBW_9 40S ribosomal protein S15a (chains J)
MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGK
IVVNLTGRLNKCGVISPRFDVQLKDLEKWQNNLLPSRQFGFIVLTTSAGIMDHEEARRKH
TGGKILGFFF
Sequence of entity 10 (M), FASTA
>6YBW_10 40S ribosomal protein S17 (chains M)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGPV
Sequence of entity 11 (L), FASTA
>6YBW_11 40S ribosomal protein S2 (chains L)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
Sequence of entity 12 (O), FASTA
>6YBW_12 40S ribosomal protein S3a (chains O)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
| MG | Magnesium ion | Mg | 60 |
Primary citation
Structure of a human 48Stranslational initiation complex. Brito Querido, J., Sokabe, M., Kraatz, S. et al. Science (2020) 369:1220-1227. DOI 10.1126/science.aba4904 · PubMed
Other PDB entries of the same protein (UniProt P62701 (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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