› 6t59

Electron Microscopy
3.11Å resolution

Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 and nascent chain-associated complex

Released:
DOI: 10.2210/pdb6t59/pdb
PDB entry 6t59 coloured by chain, front view.
PDB entry 6t59 coloured by chain, side view.
PDB entry 6t59 coloured by chain, top view.
Source organisms:
Primary publication:
TTC5 mediates autoregulation of tubulin via mRNA degradation.
Lin Z, Gasic I, Chandrasekaran V, Peters N, Shao S, Mitchison TJ, Hegde RS
Science 367 100-104 (2020)
PMID: 31727855
Related structures: EMD-10380

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
PDBe Complex ID:
PDB-CPX-243276 (preferred)
Entry contents:
49 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (53 distinct):
Large ribosomal subunit protein uL2 Chain: A3
Molecule details ›
Chain: A3
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TT27 (Residues: 1-217; Coverage: 85%)
Gene name: RPL8
Sequence domains:
Large ribosomal subunit protein uL3 Chain: B3
Molecule details ›
Chain: B3
Length: 403 amino acids
Theoretical weight: 46.11 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TL06 (Residues: 1-403; Coverage: 100%)
Gene name: RPL3
Sequence domains: Ribosomal protein L3
uL4 Chain: C3
Molecule details ›
Chain: C3
Length: 425 amino acids
Theoretical weight: 47.73 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein Chain: D3
Molecule details ›
Chain: D3
Length: 297 amino acids
Theoretical weight: 34.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SYJ6 (Residues: 1-297; Coverage: 100%)
Sequence domains:
Large ribosomal subunit protein eL6 Chain: E3
Molecule details ›
Chain: E3
Length: 291 amino acids
Theoretical weight: 33.03 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SKF7 (Residues: 1-291; Coverage: 100%)
Gene name: RPL6
Sequence domains:
Large ribosomal subunit protein uL30 Chain: F3
Molecule details ›
Chain: F3
Length: 247 amino acids
Theoretical weight: 29.2 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TUB1 (Residues: 2-246; Coverage: 100%)
Sequence domains:
eL8 Chain: G3
Molecule details ›
Chain: G3
Length: 319 amino acids
Theoretical weight: 36.22 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL6 Chain: H3
Molecule details ›
Chain: H3
Length: 192 amino acids
Theoretical weight: 21.87 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SWI6 (Residues: 1-192; Coverage: 100%)
Gene name: RPL9
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL16 Chain: I3
Molecule details ›
Chain: I3
Length: 214 amino acids
Theoretical weight: 24.64 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZQ2 (Residues: 1-214; Coverage: 100%)
Gene name: RPL10
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL5 Chain: J3
Molecule details ›
Chain: J3
Length: 178 amino acids
Theoretical weight: 20.29 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TUB8 (Residues: 1-178; Coverage: 100%)
Gene name: RPL11
Sequence domains:
eL13 Chain: L3
Molecule details ›
Chain: L3
Length: 211 amino acids
Theoretical weight: 24.33 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL14 Chain: M3
Molecule details ›
Chain: M3
Length: 218 amino acids
Theoretical weight: 23.87 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ12 (Residues: 1-218; Coverage: 100%)
Gene name: RPL14
Sequence domains: Ribosomal protein L14
Large ribosomal subunit protein eL15 Chain: N3
Molecule details ›
Chain: N3
Length: 204 amino acids
Theoretical weight: 24.21 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T0C1 (Residues: 1-204; Coverage: 100%)
Gene name: RPL15
Sequence domains: Ribosomal L15
uL13 Chain: O3
Molecule details ›
Chain: O3
Length: 203 amino acids
Theoretical weight: 23.53 KDa
Source organism: Oryctolagus cuniculus
uL22 Chain: P3
Molecule details ›
Chain: P3
Length: 184 amino acids
Theoretical weight: 21.44 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TVT6 (Residues: 1-213; Coverage: 86%)
Sequence domains: Ribosomal protein L22p/L17e
eL18 Chain: Q3
Molecule details ›
Chain: Q3
Length: 188 amino acids
Theoretical weight: 21.65 KDa
Source organism: Oryctolagus cuniculus
eL19 Chain: R3
Molecule details ›
Chain: R3
Length: 196 amino acids
Theoretical weight: 23.54 KDa
Source organism: Oryctolagus cuniculus
eL20 Chain: S3
Molecule details ›
Chain: S3
Length: 176 amino acids
Theoretical weight: 20.83 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL21 Chain: T3
Molecule details ›
Chain: T3
Length: 160 amino acids
Theoretical weight: 18.61 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SHQ2 (Residues: 1-160; Coverage: 100%)
Gene name: RPL21
Sequence domains: Ribosomal protein L21e
eL22 Chain: U3
Molecule details ›
Chain: U3
Length: 128 amino acids
Theoretical weight: 14.81 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL14 Chain: V3
Molecule details ›
Chain: V3
Length: 140 amino acids
Theoretical weight: 14.89 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T6D1 (Residues: 1-140; Coverage: 100%)
Gene name: RPL23
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL24 Chain: W3
Molecule details ›
Chain: W3
Length: 157 amino acids
Theoretical weight: 17.83 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SE28 (Residues: 1-157; Coverage: 100%)
Gene name: RPL24
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL23 Chain: X3
Molecule details ›
Chain: X3
Length: 156 amino acids
Theoretical weight: 17.77 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SE76 (Residues: 1-156; Coverage: 100%)
Gene name: RPL23A
Sequence domains:
Large ribosomal subunit protein uL24 Chain: Y3
Molecule details ›
Chain: Y3
Length: 145 amino acids
Theoretical weight: 17.3 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SQH0 (Residues: 1-145; Coverage: 100%)
Gene name: RPL26
Sequence domains:
Large ribosomal subunit protein eL27 Chain: Z3
Molecule details ›
Chain: Z3
Length: 136 amino acids
Theoretical weight: 15.84 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TXF6 (Residues: 1-136; Coverage: 100%)
Gene name: RPL27
Sequence domains:
Large ribosomal subunit protein uL15 Chain: a3
Molecule details ›
Chain: a3
Length: 148 amino acids
Theoretical weight: 16.62 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SNY0 (Residues: 1-148; Coverage: 100%)
Gene name: RPL27A
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL29 Chain: b3
Molecule details ›
Chain: b3
Length: 226 amino acids
Theoretical weight: 24.93 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGR6 (Residues: 1-226; Coverage: 92%)
Gene name: RPL29
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein eL30 Chain: c3
Molecule details ›
Chain: c3
Length: 115 amino acids
Theoretical weight: 12.81 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDL2 (Residues: 1-115; Coverage: 100%)
Gene name: RPL30
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL31 Chain: d3
Molecule details ›
Chain: d3
Length: 125 amino acids
Theoretical weight: 14.49 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SHG0 (Residues: 1-125; Coverage: 100%)
Gene name: RPL31
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chain: e3
Molecule details ›
Chain: e3
Length: 135 amino acids
Theoretical weight: 15.9 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TUN8 (Residues: 23-157; Coverage: 86%)
Gene name: RPL32
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33 Chain: f3
Molecule details ›
Chain: f3
Length: 110 amino acids
Theoretical weight: 12.58 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SF08 (Residues: 1-110; Coverage: 100%)
Gene name: RPL35A
Sequence domains: Ribosomal protein L35Ae
eL34 Chain: g3
Molecule details ›
Chain: g3
Length: 116 amino acids
Theoretical weight: 13.2 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U945 (Residues: 13-128; Coverage: 90%)
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein uL29 Chain: h3
Molecule details ›
Chain: h3
Length: 123 amino acids
Theoretical weight: 14.57 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SIT5 (Residues: 1-123; Coverage: 100%)
Gene name: RPL35
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36 Chain: i3
Molecule details ›
Chain: i3
Length: 105 amino acids
Theoretical weight: 12.26 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TTQ5 (Residues: 26-99; Coverage: 75%)
Gene name: RPL36
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37 Chain: j3
Molecule details ›
Chain: j3
Length: 97 amino acids
Theoretical weight: 11.11 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: U3KPD5 (Residues: 1-97; Coverage: 100%)
Gene name: RPL37
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL38 Chain: k3
Molecule details ›
Chain: k3
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U001 (Residues: 1-70; Coverage: 100%)
Gene name: RPL38
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL39 Chain: l3
Molecule details ›
Chain: l3
Length: 51 amino acids
Theoretical weight: 6.46 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TTN1 (Residues: 1-51; Coverage: 100%)
Sequence domains: Ribosomal L39 protein
eL40 Chain: m3
Molecule details ›
Chain: m3
Length: 102 amino acids
Theoretical weight: 11.7 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein eS32 Chain: n3
Molecule details ›
Chain: n3
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A087WNH4 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
Large ribosomal subunit protein eL42 Chain: o3
Molecule details ›
Chain: o3
Length: 106 amino acids
Theoretical weight: 12.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T040 (Residues: 1-100; Coverage: 90%)
Gene name: RPL36A
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL43 Chain: p3
Molecule details ›
Chain: p3
Length: 92 amino acids
Theoretical weight: 10.3 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SY53 (Residues: 1-92; Coverage: 100%)
Gene name: RPL37A
Sequence domains: Ribosomal L37ae protein family
Large ribosomal subunit protein eL28 Chain: r3
Molecule details ›
Chain: r3
Length: 137 amino acids
Theoretical weight: 15.78 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7L1 (Residues: 1-137; Coverage: 100%)
Gene name: RPL28
Sequence domains: Ribosomal L28e protein family
uL10 Chain: s3
Molecule details ›
Chain: s3
Length: 318 amino acids
Theoretical weight: 34.38 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL11 Chain: t3
Molecule details ›
Chain: t3
Length: 165 amino acids
Theoretical weight: 17.85 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SMR7 (Residues: 1-165; Coverage: 100%)
Gene name: RPL12
Sequence domains:
Nascent polypeptide-associated complex subunit alpha N-terminal region Chain: NI
Molecule details ›
Chain: NI
Length: 29 amino acids
Theoretical weight: 2.15 KDa
Source organism: Oryctolagus cuniculus
Nascent polypeptide-associated complex subunit alpha Chain: NA
Molecule details ›
Chain: NA
Length: 215 amino acids
Theoretical weight: 23.41 KDa
Source organism: Oryctolagus cuniculus
Transcription factor BTF3 Chain: NB
Molecule details ›
Chain: NB
Length: 206 amino acids
Theoretical weight: 22.17 KDa
Source organism: Oryctolagus cuniculus
Tetratricopeptide repeat protein 5 Chain: TT
Molecule details ›
Chain: TT
Length: 440 amino acids
Theoretical weight: 48.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8N0Z6 (Residues: 1-440; Coverage: 100%)
Gene name: TTC5
Sequence domains: Tetratricopeptide repeat protein 5 OB fold domain
Tubulin Beta Chain: 1
Molecule details ›
Chain: 1
Length: 64 amino acids
Theoretical weight: 7.16 KDa
Source organism: Oryctolagus cuniculus
P-site tRNA Chain: 23
Molecule details ›
Chain: 23
Length: 76 nucleotides
Theoretical weight: 24.44 KDa
Sequence domains: tRNA
28S ribosomal RNA Chain: 54
Molecule details ›
Chain: 54
Length: 3543 nucleotides
Theoretical weight: 1148.12 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: 74
Molecule details ›
Chain: 74
Length: 120 nucleotides
Theoretical weight: 38.69 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: 84
Molecule details ›
Chain: 84
Length: 156 nucleotides
Theoretical weight: 50.14 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 220 x MG
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.11Å
Relevant EMDB volumes: EMD-10380
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Ribosome dynamics and mRNA turnover, a complex relationship under constant cellular scrutiny.
Morris et al. (2021)
9 more

6 mentions without citation

TTC5 mediates autoregulation of tubulin via mRNA degradation.
Lin et al. (2020)
5 more