8BHF: Stalled rabbit 80S ribosomes
Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4. Determined by electron microscopy at 3.1 Å resolution. Released 6 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organisms
- Oryctolagus cuniculus, Homo sapiens
- Chains
- 86
- Atoms
- 219,017
- Mol. weight
- 3706.65 kDa
- Ligands
- MG, ZN
- Released
- 6 Sept 2023
Explore 8BHF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8BHF contains 563 α-helices and 566 β-strands across 79 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: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-22 | 20 | |
Chain A1: 12 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-11 | 9 | |
| α-helix | 17-31 | 15 | |
| β-strand | 36-39 | 4 | 1 |
| α-helix | 45-51 | 7 | |
| β-strand | 59-67 | 9 | 1 |
| α-helix | 76-78 | 3 | |
| α-helix | 84-86 | 3 | |
| α-helix | 98-109 | 12 | |
| β-strand | 114-123 | 10 | 1 |
| β-strand | 127-135 | 9 | 1 |
| α-helix | 140-143 | 4 | |
| α-helix | 154-156 | 3 | |
| α-helix | 159-162 | 4 | |
| α-helix | 166-169 | 4 | |
| α-helix | 181-183 | 3 | |
| α-helix | 188-195 | 8 | |
| β-strand | 198-200 | 3 | 2 |
Chain a3: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 47 | 1 | 106 |
| β-strand | 50 | 1 | 72 |
| α-helix | 52-61 | 10 | |
| α-helix | 62-64 | 3 | |
| β-strand | 68 | 1 | 107 |
| α-helix | 70-77 | 8 | |
| β-strand | 79 | 1 | 106 |
| α-helix | 81-93 | 13 | |
| β-strand | 98-101 | 4 | 107 |
| β-strand | 108-110 | 3 | 107 |
Chain b1: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 13 |
| β-strand | 7-12 | 6 | 14 |
| β-strand | 17-25 | 9 | 14 |
| α-helix | 26-32 | 7 | |
| α-helix | 36-45 | 10 | |
| α-helix | 64 | 1 | |
| β-strand | 65-72 | 8 | 14 |
| β-strand | 80-87 | 8 | 14 |
| β-strand | 92-93 | 2 | 13 |
Chain B1: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-10 | 5 | 9 |
| β-strand | 14 | 1 | 10 |
| β-strand | 15 | 1 | 11 |
| α-helix | 16-28 | 13 | |
| β-strand | 32-36 | 5 | 9 |
| α-helix | 38-40 | 3 | |
| β-strand | 42-44 | 3 | 11 |
| α-helix | 47-59 | 13 | |
| α-helix | 76-87 | 12 | |
| α-helix | 93-100 | 8 | |
| β-strand | 102-104 | 3 | 9 |
| β-strand | 118 | 1 | 9 |
| β-strand | 119 | 1 | 12 |
| β-strand | 124 | 1 | 10 |
| α-helix | 125-128 | 4 | |
| β-strand | 135-137 | 3 | 11 |
| α-helix | 138-145 | 8 | |
| α-helix | 151-185 | 35 | |
| α-helix | 190-198 | 9 | |
Chain b3: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 112 |
| β-strand | 28 | 1 | 34 |
| β-strand | 29-31 | 3 | 112 |
| β-strand | 36-43 | 8 | 113 |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 33 |
| α-helix | 63-65 | 3 | |
| β-strand | 66-73 | 8 | 113 |
| α-helix | 75-80 | 6 | |
| α-helix | 96-99 | 4 | |
Chain B3: 13 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-11 | 2 | |
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 109 |
| α-helix | 35-37 | 3 | |
| β-strand | 38 | 1 | 110 |
| α-helix | 41-42 | 2 | |
| β-strand | 48 | 1 | 109 |
| β-strand | 49 | 1 | 110 |
| α-helix | 51-66 | 16 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 111 |
| α-helix | 84-94 | 11 | |
| α-helix | 96 | 1 | |
| β-strand | 97-100 | 4 | 111 |
| α-helix | 103-104 | 2 | |
| β-strand | 121-124 | 4 | 111 |
| α-helix | 131-136 | 6 | |
| β-strand | 144-148 | 5 | 111 |
| β-strand | 159-162 | 4 | 111 |
| α-helix | 168-186 | 19 | |
| α-helix | 199-202 | 4 | |
| α-helix | 207-217 | 11 | |
Chain c1: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-14 | 5 | |
| α-helix | 20-32 | 13 | |
| β-strand | 37-38 | 2 | 23 |
| α-helix | 39 | 1 | |
| β-strand | 45-51 | 7 | 23 |
| β-strand | 54-57 | 4 | 23 |
| β-strand | 63-65 | 3 | 23 |
| α-helix | 74-91 | 18 | |
71 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 |
|---|
| Ribosomal protein L15 | A1 | protein | 203 | Oryctolagus cuniculus | G1T0C1 (AlphaFold model) |
| 60S ribosomal protein L13a | B1 | protein | 199 | Oryctolagus cuniculus | |
| 60S ribosomal protein L17 | C1 | protein | 153 | Oryctolagus cuniculus | G1SCJ6 (AlphaFold model) |
| Ribosomal protein L18 | D1 | protein | 187 | Oryctolagus cuniculus | |
| Ribosomal protein L19 | E1 | protein | 180 | Oryctolagus cuniculus | G1TYL6 (AlphaFold model) |
| 60S ribosomal protein L18a | F1 | protein | 176 | Oryctolagus cuniculus | |
| 60S ribosomal protein L21 | G1 | protein | 159 | Oryctolagus cuniculus | G1SHQ2 (AlphaFold model) |
| 60S ribosomal protein L22 | H1 | protein | 99 | Oryctolagus cuniculus | |
| 60S ribosomal protein L23 | I1 | protein | 139 | Oryctolagus cuniculus | |
| TRASH domain-containing protein | J1 | protein | 106 | Oryctolagus cuniculus | |
| Ribosomal protein L23/L25 N-terminal domain-containing protein | K1 | protein | 118 | Oryctolagus cuniculus | G1SE76 |
| Ribosomal protein L26 | L1 | protein | 134 | Oryctolagus cuniculus | G1SQH0 |
74 more molecules are not listed.
Sequence of entity 1 (A1), FASTA
>8BHF_1 Ribosomal protein L15 (chains A1)
GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVI
YRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWV
GEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKFH
HTIGGSRRAAWRRRNTLQLHRYR
Sequence of entity 2 (B1), FASTA
>8BHF_2 60S ribosomal protein L13a (chains B1)
QVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNT
NPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAAL
KVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKN
VEKKISKFTDVLKTHGLLV
Sequence of entity 3 (C1), FASTA
>8BHF_3 60S ribosomal protein L17 (chains C1)
VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPFR
RYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNK
APKMRRRTYRAHGRINPYMSSPCHIEMILTEKE
Sequence of entity 4 (D1), FASTA
>8BHF_4 Ribosomal protein L18 (chains D1)
GVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPL
SLSRMIRKMKLPGRENKTAVVVGTVTDDVRVQEVPKLKVCALRVTSRARSRILKAGGKIL
TFDQLALDSPKGRGTVLLSGPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGRR
ASRGYKN
Sequence of entity 5 (E1), FASTA
>8BHF_5 Ribosomal protein L19 (chains E1)
SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRA
RCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYH
SLYLKVKGNVFKNKRILMEHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKK
Sequence of entity 6 (F1), FASTA
>8BHF_6 60S ribosomal protein L18a (chains F1)
MKASGTLREYKVVGRCLPTPKCRTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGE
IVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRAR
AHSIQIMKVEEIAASKCRRPAVKQFHDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF
Sequence of entity 7 (G1), FASTA
>8BHF_7 60S ribosomal protein L21 (chains G1)
TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGKT
GRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKE
KGTWVQLKRQPAPPREAHFVRTNGKEPELLEPIPYEFMA
Sequence of entity 8 (H1), FASTA
>8BHF_8 60S ribosomal protein L22 (chains H1)
QLLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVSLERSKSKITVTSEV
PFSKRYLKYLTKKYLKKNNLRDWLRVVANTKESYELRYF
Sequence of entity 9 (I1), FASTA
>8BHF_9 60S ribosomal protein L23 (chains I1)
SKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDMV
MATVKKGKPELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNKGEMKGSAITGPV
AKECADLWPRIASNAGSIA
Sequence of entity 10 (J1), FASTA
>8BHF_10 TRASH domain-containing protein (chains J1)
MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHK
KGQQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQA
Sequence of entity 11 (K1), FASTA
>8BHF_11 Ribosomal protein L23/L25 N-terminal domain-containing protein (chains K1)
KIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAMKKIEDNNTLVF
IVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII
Sequence of entity 12 (L1), FASTA
>8BHF_12 Ribosomal protein L26 (chains L1)
MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRG
HYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILE
RKAKSRQVGKEKGK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 275 |
| ZN | Zinc ion | Zn | 7 |
Primary citation
Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4. Gangwar, S.P., Yen, L.Y., Yelshanskaya, M.V. et al. Nat Struct Mol Biol (2023).
Other PDB entries of the same protein (UniProt G1T0C1 (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
- 11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
- 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…
- 8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
- 8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
- 8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
- 8B6C 2.79 Å, Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative…
- 6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
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