5dge

X-ray diffraction
3.45Å resolution

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

Released:
Model geometry
Fit model/data
Entry authors: Melnikov S, Mailliot J, Shin B-S, Rigger L, Yusupova G, Micura R, Dever TE, Yusupov M

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 165-mer (preferred)
PDBe Complex ID:
PDB-CPX-126881 (preferred)
Entry contents:
79 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (84 distinct):
Small ribosomal subunit protein uS2A Chains: S0, s0
Molecule details ›
Chains: S0, s0
Length: 251 amino acids
Theoretical weight: 27.92 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32905 (Residues: 2-252; Coverage: 100%)
Gene names: NAB1, NAB1A, RPS0A, YGR214W, YST1
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1A Chains: S1, s1
Molecule details ›
Chains: S1, s1
Length: 254 amino acids
Theoretical weight: 28.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33442 (Residues: 2-255; Coverage: 100%)
Gene names: L9753.9, PLC1, RPS10A, RPS1A, YLR441C
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 Chains: C0, c0
Small ribosomal subunit protein uS17A Chains: C1, c1
Small ribosomal subunit protein eS12 Chains: C2, c2
Small ribosomal subunit protein uS15 Chains: C3, c3
Small ribosomal subunit protein uS11A Chains: C4, c4
Small ribosomal subunit protein uS19 Chains: C5, 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 Chains: SR, sR
Suppressor protein STM1 Chains: SM, 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 Chains: L8, 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 Chains: N4, 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
Large ribosomal subunit protein uL11A Chain: m2
Large ribosomal subunit protein uL10 Chain: p0
Large ribosomal subunit protein P1A Chains: p1, p2
Eukaryotic translation initiation factor 5A-1 Chain: f
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
DNA (5'-R(*CP*CP*(NA))-3') Chains: B, C

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 438Å b: 289.05Å c: 305.26Å
α: 90° β: 98.95° γ: 90°
R-values:
R R work R free
0.208 0.207 0.262