8QYX: Human 60S ribosomal subunit
Human 60S ribosomal subunit. Determined by electron microscopy at 1.78 Å resolution. Released 11 Dec 2024.
- Method
- Electron microscopy
- Resolution
- 1.78 Å
- Organism
- Homo sapiens
- Chains
- 44
- Atoms
- 149,908
- Mol. weight
- 2564.9 kDa
- Ligands
- ATP, SPM, SPD, ZN
- Released
- 11 Dec 2024
Explore 8QYX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8QYX contains 357 α-helices and 300 β-strands across 41 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 a1: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-24 | 5 | 5 |
| β-strand | 30-34 | 5 | 5 |
| α-helix | 35-39 | 5 | |
| α-helix | 41-42 | 2 | |
| β-strand | 43 | 1 | 6 |
| α-helix | 44 | 1 | |
| β-strand | 52 | 1 | 6 |
| α-helix | 53 | 1 | |
| α-helix | 61-66 | 6 | |
| α-helix | 69-72 | 4 | |
| α-helix | 84-114 | 31 | |
Chain A1: 15 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-78 | 52 | |
| β-strand | 81-83 | 3 | 1 |
| α-helix | 84-87 | 4 | |
| β-strand | 89-94 | 6 | 2 |
| α-helix | 103-111 | 9 | |
| β-strand | 119-124 | 6 | 2 |
| α-helix | 127-135 | 9 | |
| α-helix | 137-139 | 3 | |
| β-strand | 140-143 | 4 | 2 |
| α-helix | 147-157 | 11 | |
| β-strand | 159-162 | 4 | 3 |
| β-strand | 165-168 | 4 | 3 |
| α-helix | 172-179 | 8 | |
| α-helix | 180-182 | 3 | |
| α-helix | 187-196 | 10 | |
| α-helix | 201-207 | 7 | |
| β-strand | 208 | 1 | 3 |
| α-helix | 209-210 | 2 | |
| β-strand | 211-212 | 2 | 2 |
| α-helix | 213-215 | 3 | |
| β-strand | 226 | 1 | 4 |
| α-helix | 227-229 | 3 | |
| β-strand | 233 | 1 | 4 |
| β-strand | 234-235 | 2 | 2 |
| α-helix | 237-239 | 3 | |
| α-helix | 240-247 | 8 | |
Chain b1: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| α-helix | 14-36 | 23 | |
| α-helix | 41-72 | 32 | |
| α-helix | 89-92 | 4 | |
| α-helix | 97-100 | 4 | |
| α-helix | 105-113 | 9 | |
| α-helix | 115-118 | 4 | |
| β-strand | 119-121 | 3 | 28 |
Chain B1: 19 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-38 | 3 | |
| α-helix | 45-47 | 3 | |
| α-helix | 52-54 | 3 | |
| β-strand | 56 | 1 | 7 |
| α-helix | 59-73 | 15 | |
| β-strand | 75-76 | 2 | 8 |
| α-helix | 78-81 | 4 | |
| α-helix | 82-84 | 3 | |
| α-helix | 86-88 | 3 | |
| α-helix | 89-100 | 12 | |
| α-helix | 103-105 | 3 | |
| α-helix | 107-116 | 10 | |
| α-helix | 132-134 | 3 | |
| β-strand | 137-138 | 2 | 9 |
| α-helix | 140-148 | 9 | |
| β-strand | 154-158 | 5 | 9 |
| α-helix | 164-166 | 3 | |
| α-helix | 170-177 | 8 | |
| β-strand | 181-184 | 4 | 9 |
| α-helix | 187-193 | 7 | |
| β-strand | 201-204 | 4 | 9 |
| α-helix | 212-222 | 11 | |
| α-helix | 223-227 | 5 | |
| α-helix | 230-233 | 4 | |
| β-strand | 238-239 | 2 | 8 |
| α-helix | 244-257 | 14 | |
Chain c1: 9 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 14 |
| β-strand | 13 | 1 | 14 |
| α-helix | 18 | 1 | |
| β-strand | 19 | 1 | 27 |
| α-helix | 20-21 | 2 | |
| α-helix | 23-25 | 3 | |
| α-helix | 26-29 | 4 | |
| α-helix | 32-34 | 3 | |
| α-helix | 35-48 | 14 | |
| α-helix | 52-62 | 11 | |
| α-helix | 66-77 | 12 | |
| α-helix | 80-101 | 22 | |
Chain C1: 5 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-11 | 9 | 10 |
| β-strand | 17-21 | 5 | 11 |
| β-strand | 24-29 | 6 | 11 |
| β-strand | 32-37 | 6 | 11 |
| β-strand | 44-48 | 5 | 10 |
| β-strand | 54-62 | 9 | 10 |
| α-helix | 64-85 | 22 | |
| β-strand | 88-95 | 8 | 12 |
| β-strand | 102-106 | 5 | 13 |
| β-strand | 111-115 | 5 | 13 |
| α-helix | 117-119 | 3 | |
| α-helix | 122-123 | 2 | |
| β-strand | 124-127 | 4 | 13 |
| α-helix | 128-129 | 2 | |
| β-strand | 133-136 | 4 | 12 |
| β-strand | 143-148 | 6 | 12 |
| α-helix | 151-164 | 14 | |
| β-strand | 178-185 | 8 | 12 |
Chain d1: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| β-strand | 16-17 | 2 | 19 |
| β-strand | 27-28 | 2 | 19 |
| β-strand | 33-34 | 2 | 19 |
| α-helix | 44-45 | 2 | |
| α-helix | 51-56 | 6 | |
| α-helix | 67-74 | 8 | |
| α-helix | 84-86 | 3 | |
Chain D1: 11 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 6-9 | 4 | |
| α-helix | 15-16 | 2 | |
| α-helix | 26-29 | 4 | |
| β-strand | 35-37 | 3 | 15 |
| β-strand | 48-54 | 7 | 15 |
| β-strand | 58-61 | 4 | 16 |
| α-helix | 62-80 | 19 | |
| β-strand | 85-89 | 5 | 15 |
| β-strand | 95-99 | 5 | 16 |
| α-helix | 119-120 | 2 | |
| β-strand | 121-129 | 9 | 16 |
| β-strand | 134-140 | 7 | 15 |
| α-helix | 142-144 | 3 | |
| α-helix | 145-155 | 11 | |
| α-helix | 156-158 | 3 | |
| β-strand | 163-167 | 5 | 15 |
| β-strand | 170 | 1 | 17 |
| β-strand | 177 | 1 | 17 |
| α-helix | 178-186 | 9 | |
| β-strand | 190-193 | 4 | 18 |
| β-strand | 196-199 | 4 | 18 |
| α-helix | 206-211 | 6 | |
33 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 |
|---|
| Large ribosomal subunit protein uL30 | A1 | protein | 248 | Homo sapiens | P18124 (AlphaFold model) |
| 60S ribosomal protein L7a | B1 | protein | 266 | Homo sapiens | P62424 (AlphaFold model) |
| 60S ribosomal protein L9 | C1 | protein | 192 | Homo sapiens | P32969 (AlphaFold model) |
| Ribosomal protein uL16-like | D1 | protein | 214 | Homo sapiens | Q96L21 (AlphaFold model) |
| 60S ribosomal protein L11 | E1 | protein | 178 | Homo sapiens | P62913 |
| 60S ribosomal protein L13 | F1 | protein | 211 | Homo sapiens | P26373 |
| 60S ribosomal protein L14 | G1 | protein | 215 | Homo sapiens | P50914 |
| 60S ribosomal protein L15 | H1 | protein | 204 | Homo sapiens | P61313 |
| 60S ribosomal protein L13a | I1 | protein | 203 | Homo sapiens | P40429 |
| 60S ribosomal protein L17 | J1 | protein | 184 | Homo sapiens | P18621 |
| 60S ribosomal protein L18 | K1 | protein | 188 | Homo sapiens | Q07020 |
| 60S ribosomal protein L19 | L1 | protein | 196 | Homo sapiens | P84098 |
32 more molecules are not listed.
Sequence of entity 1 (A1), FASTA
>8QYX_1 Large ribosomal subunit protein uL30 (chains A1)
MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKE
YRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNG
TFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLG
KYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQI
NRLIRRMN
Sequence of entity 2 (B1), FASTA
>8QYX_2 60S ribosomal protein L7a (chains B1)
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRY
IRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK
KAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVP
YCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGN
VLGPKSVARIAKLEKAKAKELATKLG
Sequence of entity 3 (C1), FASTA
>8QYX_3 60S ribosomal protein L9 (chains C1)
MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 4 (D1), FASTA
>8QYX_4 Ribosomal protein uL16-like (chains D1)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLGGHMVSDEYEQL
SSEALEAARICANKYMVKSCGRDGFHMRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNEEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAKKCLIPDGCGVKYVPSHGPLDKWRVLHS
Sequence of entity 5 (E1), FASTA
>8QYX_5 60S ribosomal protein L11 (chains E1)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
Sequence of entity 6 (F1), FASTA
>8QYX_6 60S ribosomal protein L13 (chains F1)
MAPSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPVRNVYKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK
Sequence of entity 7 (G1), FASTA
>8QYX_7 60S ribosomal protein L14 (chains G1)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMPFKCMQLTDF
ILKFPHSAHQKYVRQAWQKADINTKWAATRWAKKIEARERKAKMTDFDRFKVMKAKKMRN
RIIKNEVKKLQKAALLKASPKKAPGTKGTAAAAAAAAAAKVPAKKITAASKKAPAQKVPA
QKATGQKAAPAPKAQKGQKAPAQKAPAPKASGKKA
Sequence of entity 8 (H1), FASTA
>8QYX_8 60S ribosomal protein L15 (chains H1)
MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYV
IYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYW
VGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKF
HHTIGGSRRAAWRRRNTLQLHRYR
Sequence of entity 9 (I1), FASTA
>8QYX_9 60S ribosomal protein L13a (chains I1)
MAEVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRK
RMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVV
PAALKVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQ
AEKNVEKKIDKYTEVLKTHGLLV
Sequence of entity 10 (J1), FASTA
>8QYX_10 60S ribosomal protein L17 (chains J1)
MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPF
RRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVN
KAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKL
MARE
Sequence of entity 11 (K1), FASTA
>8QYX_11 60S ribosomal protein L18 (chains K1)
MGVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPP
LSLSRMIRKMKLPGRENKTAVVVGTITDDVRVQEVPKLKVCALRVTSRARSRILRAGGKI
LTFDQLALDSPKGCGTVLLSGPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGR
RASRGYKN
Sequence of entity 12 (L1), FASTA
>8QYX_12 60S ribosomal protein L19 (chains L1)
MSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSR
ARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMY
HSLYLKVKGNVFKNKRILMEHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAK
KEEIIKTLSKEEETKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| SPM | Spermine | C10 H26 N4 | 5 |
| SPD | Spermidine | C7 H19 N3 | 7 |
| ZN | Zinc ion | Zn | 5 |
| PUT | 1,4-diaminobutane | C4 H12 N2 | 7 |
| MG | Magnesium ion | Mg | 186 |
Water and common crystallization additives (K) are not listed.
Primary citation
Visualizing the modification landscape of the human 60S ribosomal subunit at close to atomic resolution. Wiechert, F., Unbehaun, A., Sprink, T. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkae1191 · PubMed
Other PDB entries of the same protein (UniProt P18124 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
- 8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
- 29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
- 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
- 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)
- 29IX 2.2 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. NT-2 added to purified…
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