5mei

X-ray diffraction
3.5Å resolution

Crystal structure of Agelastatin A bound to the 80S ribosome

Released:
Model geometry
Fit model/data

Function and Biology Details

Structure analysis Details

Assemblies composition:
hetero 79-mer
hetero 80-mer (preferred)
PDBe Complex ID:
PDB-CPX-249660 (preferred)
Entry contents:
79 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (83 distinct):
Large ribosomal subunit protein uL2A Chains: CD, j
Molecule details ›
Chains: CD, j
Length: 252 amino acids
Theoretical weight: 27.22 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX45 (Residues: 2-253; Coverage: 99%)
Gene names: RPL2A, RPL5B, YFR031BC, YFR031C-A
Sequence domains:
Large ribosomal subunit protein uL3 Chains: CE, k
Molecule details ›
Chains: CE, k
Length: 386 amino acids
Theoretical weight: 43.72 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14126 (Residues: 2-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4A Chains: CF, l
Large ribosomal subunit protein uL18 Chains: CG, m
Large ribosomal subunit protein eL6A Chains: CH, n
Large ribosomal subunit protein uL30A Chains: CI, o
Large ribosomal subunit protein eL8A Chains: CJ, p
Large ribosomal subunit protein uL6A Chains: CK, q
Large ribosomal subunit protein uL16 Chains: CL, r
Large ribosomal subunit protein uL5B Chains: CM, s
Large ribosomal subunit protein eL13A Chains: CN, t
Large ribosomal subunit protein eL14A Chains: CO, u
Large ribosomal subunit protein eL15A Chains: CP, v
Large ribosomal subunit protein uL13A Chains: CQ, w
Large ribosomal subunit protein uL22A Chains: CR, x
Large ribosomal subunit protein eL18A Chains: CS, y
Large ribosomal subunit protein eL19A Chains: CT, z
Large ribosomal subunit protein eL20A Chains: 0, CU
Large ribosomal subunit protein eL21A Chains: 2, CV
Large ribosomal subunit protein eL22A Chains: 5, CW
Large ribosomal subunit protein uL14A Chains: CX, l2
Large ribosomal subunit protein eL24A Chains: 7, CY
Large ribosomal subunit protein uL23 Chains: 8, CZ
Large ribosomal subunit protein uL24A Chains: 9, DA
Large ribosomal subunit protein eL27A Chains: AA, DB
Large ribosomal subunit protein uL15 Chains: AB, DC
Large ribosomal subunit protein eL29 Chains: AC, DD
Large ribosomal subunit protein eL30 Chains: AD, DE
Large ribosomal subunit protein eL31A Chains: AE, DF
Large ribosomal subunit protein eL32 Chains: AF, DG
Large ribosomal subunit protein eL33A Chains: AG, DH
Large ribosomal subunit protein eL34A Chains: AH, DI
Large ribosomal subunit protein uL29A Chains: AI, DJ
Large ribosomal subunit protein eL36A Chains: AJ, DK
Large ribosomal subunit protein eL37A Chains: AK, DL
Large ribosomal subunit protein eL38 Chains: AL, DM
Large ribosomal subunit protein eL39 Chains: AM, DN
Large ribosomal subunit protein eL40A Chains: AN, DO
Small ribosomal subunit protein eS32A Chains: AO, DP
Large ribosomal subunit protein eL42A Chains: AP, DQ
Large ribosomal subunit protein eL43A Chains: AQ, DR
Suppressor protein STM1 Chain: i
Large ribosomal subunit protein uL10 Chain: p0
Suppressor protein STM1 Chain: sM
Small ribosomal subunit protein uS2A Chains: B, s0
Small ribosomal subunit protein eS1A Chains: C, s1
Small ribosomal subunit protein uS5 Chains: D, s2
Small ribosomal subunit protein uS3 Chains: E, s3
Small ribosomal subunit protein eS4A Chains: F, s4
Small ribosomal subunit protein uS7 Chains: G, s5
Small ribosomal subunit protein eS6A Chains: H, s6
Small ribosomal subunit protein eS7A Chains: I, s7
Small ribosomal subunit protein eS8A Chains: J, s8
Small ribosomal subunit protein uS4A Chains: K, s9
Small ribosomal subunit protein eS10A Chains: L, c0
Small ribosomal subunit protein uS17A Chains: M, c1
Small ribosomal subunit protein eS12 Chains: N, c2
Small ribosomal subunit protein uS15 Chains: O, c3
Small ribosomal subunit protein uS11B Chains: P, c4
Small ribosomal subunit protein uS19 Chains: Q, c5
Small ribosomal subunit protein uS9A Chains: R, c6
Small ribosomal subunit protein eS17B Chain: S
Small ribosomal subunit protein uS13A Chains: T, c8
Small ribosomal subunit protein eS19A Chains: U, c9
Small ribosomal subunit protein uS10 Chains: V, d0
Small ribosomal subunit protein eS21A Chains: W, d1
Small ribosomal subunit protein uS8A Chains: X, d2
Small ribosomal subunit protein uS12A Chains: Y, d3
Small ribosomal subunit protein eS24A Chains: Z, d4
Small ribosomal subunit protein eS25A Chains: a, d5
Small ribosomal subunit protein eS26B Chains: b, d6
Small ribosomal subunit protein eS27A Chains: c, d7
Small ribosomal subunit protein eS28A Chains: d, d8
Small ribosomal subunit protein uS14A Chains: d9, e
Small ribosomal subunit protein eS30A Chains: e0, f
Small ribosomal subunit protein eS31 Chain: g
Small ribosomal subunit protein RACK1 Chains: h, sR
Small ribosomal subunit protein eS17A Chain: c7
Small ribosomal subunit protein eS31 Chain: e1
25S ribosomal RNA Chains: 1, AR
5S ribosomal RNA Chains: 3, AS
5.8S ribosomal RNA Chains: 4, AT
18S Ribosomal RNA Chains: 6, A

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1, SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 304.08Å b: 286.55Å c: 436.55Å
α: 90° β: 99.05° γ: 90°
R-values:
R R work R free
0.196 0.195 0.239
Expression system: Saccharomyces cerevisiae