8PKL: Escherichia coli paused disome complex
Escherichia coli paused disome complex (leading 70S non-rotated closed PRE state). Determined by electron microscopy at 3.09 Å resolution. Released 6 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 3.09 Å
- Organism
- Escherichia coli
- Chains
- 60
- Atoms
- 151,734
- Mol. weight
- 2293.94 kDa
- Ligands
- ZN, PUT, SPD, MG
- Released
- 6 Mar 2024
Explore 8PKL in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8PKL contains 258 α-helices and 319 β-strands across 52 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 0: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 1 |
| β-strand | 14-17 | 4 | 1 |
| β-strand | 24-27 | 4 | 1 |
| α-helix | 31-33 | 3 | |
| β-strand | 35-37 | 3 | 1 |
Chain 1: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-18 | 6 | 5 |
| β-strand | 24-29 | 6 | 5 |
| β-strand | 33-40 | 8 | 6 |
| β-strand | 45-52 | 8 | 6 |
| α-helix | 53-62 | 10 | |
| α-helix | 64-74 | 11 | |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| α-helix | 11-33 | 23 | |
| α-helix | 41-60 | 20 | |
Chain 3: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-9 | 5 | 12 |
| α-helix | 18-27 | 10 | |
| β-strand | 35-38 | 4 | 12 |
| α-helix | 42-50 | 9 | |
| β-strand | 55-58 | 4 | 12 |
Chain 4: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-16 | 7 | 15 |
| β-strand | 21-26 | 6 | 15 |
| β-strand | 32-34 | 3 | 15 |
| α-helix | 42-45 | 4 | |
| α-helix | 56-63 | 8 | |
Chain 5: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 10-16 | 7 | |
| α-helix | 17-19 | 3 | |
| β-strand | 29-30 | 2 | 18 |
| β-strand | 37-38 | 2 | 18 |
| β-strand | 48-49 | 2 | 19 |
| β-strand | 52-53 | 2 | 19 |
Chain 6: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-11 | 4 | |
| β-strand | 15-16 | 2 | 24 |
| β-strand | 22-24 | 3 | 24 |
| α-helix | 38-44 | 7 | |
| β-strand | 48-49 | 2 | 24 |
| α-helix | 50-51 | 2 | |
| α-helix | 55-61 | 7 | |
Chain a: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-14 | 9 | |
| α-helix | 23-33 | 11 | |
| β-strand | 41 | 1 | 28 |
| β-strand | 43-48 | 6 | 29 |
| α-helix | 55-57 | 3 | |
| β-strand | 60-64 | 5 | 30 |
| β-strand | 160-164 | 5 | 30 |
| β-strand | 170-171 | 2 | 29 |
| β-strand | 177 | 1 | 28 |
| α-helix | 182-199 | 18 | |
| β-strand | 209-215 | 7 | 29 |
| α-helix | 219-221 | 3 | |
| β-strand | 222-223 | 2 | 29 |
44 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 |
|---|
| 50S ribosomal protein L36 | 0 | protein | 38 | Escherichia coli | P0A7Q6 (AlphaFold model) |
| 50S ribosomal protein L28 | 1 | protein | 78 | Escherichia coli | P0A7M2 (AlphaFold model) |
| 50S ribosomal protein L29 | 2 | protein | 63 | Escherichia coli | P0A7M6 (AlphaFold model) |
| 50S ribosomal protein L30 | 3 | protein | 59 | Escherichia coli | P0AG51 (AlphaFold model) |
| Large ribosomal subunit protein bL31A | 4 | protein | 70 | Escherichia coli | P0A7M9 |
| 50S ribosomal protein L32 | 5 | protein | 57 | Escherichia coli | P0A7N4 |
| 50S ribosomal protein L35 | 6 | protein | 65 | Escherichia coli | P0A7Q1 |
| 23S ribosomal RNA | 7 | RNA | 2921 | Escherichia coli | |
| 5S ribosomal RNA | 8 | RNA | 120 | Escherichia coli | |
| 16S ribosomal RNA | A | RNA | 1535 | Escherichia coli | |
| Small ribosomal subunit protein uS2 | B | protein | 241 | Escherichia coli | P0A7V0 |
| Small ribosomal subunit protein uS3 | C | protein | 233 | Escherichia coli | P0A7V3 |
48 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>8PKL_1 50S ribosomal protein L36 (chains 0)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG
Sequence of entity 2 (1), FASTA
>8PKL_2 50S ribosomal protein L28 (chains 1)
MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVID
KKGIDTVLAELRARGEKY
Sequence of entity 3 (2), FASTA
>8PKL_3 50S ribosomal protein L29 (chains 2)
MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEK
AGA
Sequence of entity 4 (3), FASTA
>8PKL_4 50S ribosomal protein L30 (chains 3)
MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE
Sequence of entity 5 (4), FASTA
>8PKL_5 Large ribosomal subunit protein bL31A (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIPGSK
Sequence of entity 6 (5), FASTA
>8PKL_6 50S ribosomal protein L32 (chains 5)
MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK
Sequence of entity 7 (6), FASTA
>8PKL_7 50S ribosomal protein L35 (chains 6)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA
Sequence of entity 8 (7), FASTA
>8PKL_8 23S ribosomal RNA (chains 7)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAAUCUUACAACGCCGAAGCUGUU
Sequence of entity 9 (8), FASTA
>8PKL_9 5S ribosomal RNA (chains 8)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAA
Sequence of entity 10 (A), FASTA
>8PKL_10 16S ribosomal RNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCAC
Sequence of entity 11 (B), FASTA
>8PKL_11 Small ribosomal subunit protein uS2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E
Sequence of entity 12 (C), FASTA
>8PKL_12 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| PUT | 1,4-diaminobutane | C4 H12 N2 | 2 |
| SPD | Spermidine | C7 H19 N3 | 1 |
| MG | Magnesium ion | Mg | 287 |
| ALA | Alanine | C3 H7 N O2 | 1 |
Primary citation
Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM. Flugel, T., Schacherl, M., Unbehaun, A. et al. Nat Commun (2024) 15:1756-1756. DOI 10.1038/s41467-024-46092-3 · PubMed
Other PDB entries of the same protein (UniProt P0A7Q6 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
- 9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
- 8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
- 8CGV 1.66 Å, Tiamulin bound to the 50S subunit
- 8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
- 8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
- 8CAM 1.86 Å, Evernimicin bound to the 50S subunit
- 9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
- 9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
- 9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
- 9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
- 9D89 1.95 Å, E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)
Browse structure collections
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