› 5lyb

X-ray diffraction
3.25Å resolution

Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn

Released:
DOI: 10.2210/pdb5lyb/pdb
Model geometry
Fit model/data
PDB entry 5lyb coloured by chain, front view.
PDB entry 5lyb coloured by chain, side view.
PDB entry 5lyb coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Molecular insights into protein synthesis with proline residues.
Melnikov S, Mailliot J, Rigger L, Neuner S, Shin BS, Yusupova G, Dever TE, Micura R, Yusupov M
EMBO Rep 17 1776-1784 (2016)
PMID: 27827794

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero 80-mer
hetero 84-mer (preferred)
PDBe Complex ID:
PDB-CPX-218873 (preferred)
Entry contents:
85 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (90 distinct):
Small ribosomal subunit protein uS2A Chains: S0, s0
Molecule details ›
Chains: S0, s0
Length: 206 amino acids
Theoretical weight: 22.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: B3LI22 (Residues: 2-207; Coverage: 82%)
Gene names: NAB1, NAB1A, RPS0A, SCRG_00807, YST1
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1A Chains: S1, s1
Molecule details ›
Chains: S1, s1
Length: 216 amino acids
Theoretical weight: 24.5 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: B3RHV0 (Residues: 20-235; Coverage: 85%)
Gene names: RPS1A, SCRG_04379
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS5 Chains: S2, s2
Small ribosomal subunit protein uS3 Chains: S3, s3
Small ribosomal subunit protein eS4A Chains: S4, s4
Small ribosomal subunit protein uS7 Chains: S5, s5
Small ribosomal subunit protein eS6A Chains: S6, s6
Small ribosomal subunit protein eS7A Chains: S7, s7
Small ribosomal subunit protein eS8A Chains: S8, s8
Small ribosomal subunit protein uS4A Chains: S9, s9
Small ribosomal subunit protein eS10A Chain: C0
Small ribosomal subunit protein uS17A Chains: C1, c1
Small ribosomal subunit protein eS12 Chain: C2
Small ribosomal subunit protein uS15 Chains: C3, c3
Small ribosomal subunit protein uS11A Chains: C4, c4
Small ribosomal subunit protein uS19 Chain: C5
Small ribosomal subunit protein uS9A Chains: C6, c6
Small ribosomal subunit protein eS17A Chains: C7, c7
Small ribosomal subunit protein uS13A Chains: C8, c8
Small ribosomal subunit protein eS19A Chains: C9, c9
Small ribosomal subunit protein uS10 Chains: D0, d0
Small ribosomal subunit protein eS21A Chains: D1, d1
Small ribosomal subunit protein uS8A Chains: D2, d2
Small ribosomal subunit protein uS12A Chains: D3, d3
Small ribosomal subunit protein eS24A Chains: D4, d4
Small ribosomal subunit protein eS25A Chains: D5, d5
Small ribosomal subunit protein eS26B Chains: D6, d6
Small ribosomal subunit protein eS27A Chains: D7, d7
Small ribosomal subunit protein eS28A Chains: D8, d8
Small ribosomal subunit protein uS14A Chains: D9, d9
Small ribosomal subunit protein eS30A Chains: E0, e0
Small ribosomal subunit protein eS31 Chains: E1, e1
Small ribosomal subunit protein RACK1 Chain: SR
Suppressor protein STM1 Chain: SM
Large ribosomal subunit protein uL2A Chains: L2, l2
Large ribosomal subunit protein uL3 Chains: L3, l3
Large ribosomal subunit protein uL4A Chains: L4, l4
Large ribosomal subunit protein uL18 Chains: L5, l5
Large ribosomal subunit protein eL6A Chains: L6, l6
Large ribosomal subunit protein uL30A Chains: L7, l7
Large ribosomal subunit protein eL8A Chain: L8
Large ribosomal subunit protein uL6A Chains: L9, l9
Large ribosomal subunit protein uL16 Chains: M0, m0
Large ribosomal subunit protein uL5B Chains: M1, m1
Large ribosomal subunit protein eL13A Chains: M3, m3
Large ribosomal subunit protein eL14A Chains: M4, m4
Large ribosomal subunit protein eL15A Chains: M5, m5
Large ribosomal subunit protein uL13A Chains: M6, m6
Large ribosomal subunit protein uL22A Chains: M7, m7
Large ribosomal subunit protein eL18A Chains: M8, m8
Large ribosomal subunit protein eL19A Chains: M9, m9
Large ribosomal subunit protein eL20A Chains: N0, n0
Large ribosomal subunit protein eL21A Chains: N1, n1
Large ribosomal subunit protein eL22A Chains: N2, n2
Large ribosomal subunit protein uL14A Chains: N3, n3
Large ribosomal subunit protein eL24A Chain: N4
Large ribosomal subunit protein uL23 Chains: N5, n5
Large ribosomal subunit protein uL24A Chains: N6, n6
Large ribosomal subunit protein eL27A Chains: N7, n7
Large ribosomal subunit protein uL15 Chains: N8, n8
Large ribosomal subunit protein eL29 Chains: N9, n9
Large ribosomal subunit protein eL30 Chains: O0, o0
Large ribosomal subunit protein eL31A Chains: O1, o1
Large ribosomal subunit protein eL32 Chains: O2, o2
Large ribosomal subunit protein eL33A Chains: O3, o3
Large ribosomal subunit protein eL34A Chains: O4, o4
Large ribosomal subunit protein uL29A Chains: O5, o5
Large ribosomal subunit protein eL36A Chains: O6, o6
Large ribosomal subunit protein eL37A Chains: O7, o7
Large ribosomal subunit protein eL38 Chains: O8, o8
Large ribosomal subunit protein eL39 Chains: O9, o9
Large ribosomal subunit protein eL40A Chains: Q0, q0
Small ribosomal subunit protein eS32A Chains: Q1, q1
Large ribosomal subunit protein eL42A Chains: Q2, q2
Large ribosomal subunit protein eL43A Chains: Q3, q3
Small ribosomal subunit protein eS10A Chain: c0
40S Ribosomal Protein S12 Chain: c2
Small ribosomal subunit protein uS19 Chain: c5
Small ribosomal subunit protein RACK1 Chain: sR
Suppressor protein STM1 Chain: sM
Large ribosomal subunit protein eL8A Chain: l8
60S Ribosomal Protein L12 Chain: m2
Large ribosomal subunit protein eL24A Chain: n4
Large ribosomal subunit protein uL10 Chain: p0
60S Ribosomal Protein P1/2 Chains: p1, p2
18S Ribosomal RNA Chains: 2, 6
25S ribosomal RNA Chains: 1, 5
5S ribosomal RNA Chains: 3, 7
5.8S ribosomal RNA Chains: 4, 8
aminoacyl-tRNA fragment ACCPmn Chains: A, a

Ligands and Environments

3 bound ligands:
Ligand MG 2192 x MG
Ligand OHX 1345 x OHX
Ligand ZN 16 x ZN
1 modified residue:
Ligand PPU 2 x PPU

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 436.18Å b: 288.24Å c: 303.58Å
α: 90° β: 98.87° γ: 90°
R-values:
R R work R free
0.209 0.208 0.249

Quick links

Citations

9 review citations

Translation Elongation and Recoding in Eukaryotes.
Dever et al. (2018)
8 more

1 mention without citation

Molecular insights into protein synthesis with proline residues.
Melnikov et al. (2016)