› 5vyc

X-ray diffraction
6Å resolution

Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1.

Released:
DOI: 10.2210/pdb5vyc/pdb
PDB entry 5vyc coloured by chain, front view.
PDB entry 5vyc coloured by chain, side view.
PDB entry 5vyc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structure of the Human Ribosome in Complex with DENR-MCT-1.
Lomakin IB, Stolboushkina EA, Vaidya AT, Zhao C, Garber MB, Dmitriev SE, Steitz TA
Cell Rep 20 521-528 (2017)
PMID: 28723557

Function and Biology Details

Reaction catalysed: 
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 37-mer (preferred)
PDBe Complex ID:
PDB-CPX-123203 (preferred)
Entry contents:
36 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (37 distinct):
Small ribosomal subunit protein eS19 Chains: T1, T2, T3, T4, T5, T6
Molecule details ›
Chains: T1, T2, T3, T4, T5, T6
Length: 145 amino acids
Theoretical weight: 16.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 1-145; Coverage: 100%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chains: U1, U2, U3, U4, U5, U6
Molecule details ›
Chains: U1, U2, U3, U4, U5, U6
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 1-119; Coverage: 100%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS21 Chains: V1, V2, V3, V4, V5, V6
Molecule details ›
Chains: V1, V2, V3, V4, V5, V6
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63220 (Residues: 1-83; Coverage: 100%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS12 Chains: X1, X2, X3, X4, X5, X6
Molecule details ›
Chains: X1, X2, X3, X4, X5, X6
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 1-143; Coverage: 100%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS26 Chains: a1, a2, a3, a4, a5, a6
Molecule details ›
Chains: a1, a2, a3, a4, a5, a6
Length: 115 amino acids
Theoretical weight: 13.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62854 (Residues: 1-115; Coverage: 100%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS28 Chains: c1, c2, c3, c4, c5, c6
Molecule details ›
Chains: c1, c2, c3, c4, c5, c6
Length: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 1-69; Coverage: 100%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14 Chains: d1, d2, d3, d4, d5, d6
Molecule details ›
Chains: d1, d2, d3, d4, d5, d6
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Ubiquitin-ribosomal protein eS31 fusion protein Chains: f1, f2, f3, f4, f5, f6
Molecule details ›
Chains: f1, f2, f3, f4, f5, f6
Length: 156 amino acids
Theoretical weight: 17.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q5RKT7 (Residues: 1-156; Coverage: 100%)
Gene name: RPS27A
Sequence domains:
Small ribosomal subunit protein RACK1 Chains: g1, g2, g3, g4, g5, g6
Molecule details ›
Chains: g1, g2, g3, g4, g5, g6
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 1-317; Coverage: 100%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein uS5 Chains: C1, C2, C3, C4, C5, C6
Molecule details ›
Chains: C1, C2, C3, C4, C5, C6
Length: 293 amino acids
Theoretical weight: 31.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 1-293; Coverage: 100%)
Gene names: RPS2, RPS4
Sequence domains:
Small ribosomal subunit protein eS6 Chains: G1, G2, G3, G4, G5, G6
Molecule details ›
Chains: G1, G2, G3, G4, G5, G6
Length: 249 amino acids
Theoretical weight: 28.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62753 (Residues: 1-249; Coverage: 100%)
Gene names: OK/SW-cl.2, RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein uS4 Chains: J1, J2, J3, J4, J5, J6
Molecule details ›
Chains: J1, J2, J3, J4, J5, J6
Length: 194 amino acids
Theoretical weight: 22.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 1-194; Coverage: 100%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein eS12 Chains: M1, M2, M3, M4, M5, M6
Molecule details ›
Chains: M1, M2, M3, M4, M5, M6
Length: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 1-132; Coverage: 100%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS15 Chains: N1, N2, N3, N4, N5, N6
Molecule details ›
Chains: N1, N2, N3, N4, N5, N6
Length: 151 amino acids
Theoretical weight: 17.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 1-151; Coverage: 100%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein uS11 Chains: O1, O2, O3, O4, O5, O6
Molecule details ›
Chains: O1, O2, O3, O4, O5, O6
Length: 151 amino acids
Theoretical weight: 16.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 1-151; Coverage: 100%)
Gene names: PRO2640, RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS8 Chains: W1, W2, W3, W4, W5, W6
Molecule details ›
Chains: W1, W2, W3, W4, W5, W6
Length: 130 amino acids
Theoretical weight: 14.87 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62244 (Residues: 1-130; Coverage: 100%)
Gene names: OK/SW-cl.82, RPS15A
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein eS24 Chains: Y1, Y2, Y3, Y4, Y5, Y6
Molecule details ›
Chains: Y1, Y2, Y3, Y4, Y5, Y6
Length: 133 amino acids
Theoretical weight: 15.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62847 (Residues: 1-133; Coverage: 100%)
Gene name: RPS24
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS25 Chains: Z1, Z2, Z3, Z4, Z5, Z6
Molecule details ›
Chains: Z1, Z2, Z3, Z4, Z5, Z6
Length: 125 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 1-125; Coverage: 100%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS27 Chains: b1, b2, b3, b4, b5, b6
Molecule details ›
Chains: b1, b2, b3, b4, b5, b6
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 1-84; Coverage: 100%)
Gene names: MPS1, RPS27
Sequence domains: Ribosomal protein S27
FAU ubiquitin like and ribosomal protein S30 fusion Chains: e1, e2, e3, e4, e5, e6
Molecule details ›
Chains: e1, e2, e3, e4, e5, e6
Length: 133 amino acids
Theoretical weight: 14.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: E9PR30 (Residues: 1-25, 26-98; Coverage: 100%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein uS2 Chains: A1, A2, A3, A4, A5, A6
Molecule details ›
Chains: A1, A2, A3, A4, A5, A6
Length: 295 amino acids
Theoretical weight: 32.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 1-295; Coverage: 100%)
Gene names: LAMBR, LAMR1, RPSA
Sequence domains:
Small ribosomal subunit protein eS1 Chains: B1, B2, B3, B4, B5, B6
Molecule details ›
Chains: B1, B2, B3, B4, B5, B6
Length: 264 amino acids
Theoretical weight: 30 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61247 (Residues: 1-264; Coverage: 100%)
Gene names: FTE1, MFTL, RPS3A
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS3 Chains: D1, D2, D3, D4, D5, D6
Molecule details ›
Chains: D1, D2, D3, D4, D5, D6
Length: 243 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 1-243; Coverage: 100%)
Gene names: OK/SW-cl.26, RPS3
Sequence domains:
Small ribosomal subunit protein eS4, X isoform Chains: E1, E2, E3, E4, E5, E6
Molecule details ›
Chains: E1, E2, E3, E4, E5, E6
Length: 263 amino acids
Theoretical weight: 29.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62701 (Residues: 1-263; Coverage: 100%)
Gene names: CCG2, RPS4, RPS4X, SCAR
Sequence domains:
Small ribosomal subunit protein uS7 Chains: F1, F2, F3, F4, F5, F6
Molecule details ›
Chains: F1, F2, F3, F4, F5, F6
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 1-204; Coverage: 100%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS7 Chains: H1, H2, H3, H4, H5, H6
Molecule details ›
Chains: H1, H2, H3, H4, H5, H6
Length: 194 amino acids
Theoretical weight: 22.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 1-194; Coverage: 100%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8 Chains: I1, I2, I3, I4, I5, I6
Molecule details ›
Chains: I1, I2, I3, I4, I5, I6
Length: 208 amino acids
Theoretical weight: 24.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62241 (Residues: 1-208; Coverage: 100%)
Gene names: OK/SW-cl.83, RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein eS10 Chains: K1, K2, K3, K4, K5, K6
Molecule details ›
Chains: K1, K2, K3, K4, K5, K6
Length: 165 amino acids
Theoretical weight: 18.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 1-165; Coverage: 100%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS17 Chains: L1, L2, L3, L4, L5, L6
Molecule details ›
Chains: L1, L2, L3, L4, L5, L6
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62280 (Residues: 1-158; Coverage: 100%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein uS19 Chains: P1, P2, P3, P4, P5, P6
Molecule details ›
Chains: P1, P2, P3, P4, P5, P6
Length: 145 amino acids
Theoretical weight: 17.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 1-145; Coverage: 100%)
Gene names: RIG, RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9 Chains: Q1, Q2, Q3, Q4, Q5, Q6
Molecule details ›
Chains: Q1, Q2, Q3, Q4, Q5, Q6
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 1-146; Coverage: 100%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17 Chains: R1, R2, R3, R4, R5, R6
Molecule details ›
Chains: R1, R2, R3, R4, R5, R6
Length: 135 amino acids
Theoretical weight: 15.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 1-135; Coverage: 100%)
Gene names: RPS17, RPS17L
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS13 Chains: S1, S2, S3, S4, S5, S6
Molecule details ›
Chains: S1, S2, S3, S4, S5, S6
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 1-152; Coverage: 100%)
Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS32 Chains: j1, j2, j3, j4, j5, j6
Molecule details ›
Chains: j1, j2, j3, j4, j5, j6
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62945 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
Malignant T-cell-amplified sequence 1 Chains: k1, k2, k3, k4, k5, k6
Molecule details ›
Chains: k1, k2, k3, k4, k5, k6
Length: 181 amino acids
Theoretical weight: 20.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9ULC4 (Residues: 1-181; Coverage: 100%)
Gene names: MCT1, MCTS1
Sequence domains:
Density-regulated protein Chains: l1, l2, l3, l4, l5, l6
Molecule details ›
Chains: l1, l2, l3, l4, l5, l6
Length: 198 amino acids
Theoretical weight: 22.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O43583 (Residues: 1-198; Coverage: 100%)
Gene names: DENR, DRP1, H14
Sequence domains:
18S Ribosomal RNA Chains: i1, i2, i3, i4, i5, i6
Molecule details ›
Chains: i1, i2, i3, i4, i5, i6
Length: 1869 nucleotides
Theoretical weight: 602.75 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 334.67Å b: 597.13Å c: 336.5Å
α: 90° β: 120.29° γ: 90°
R-values:
R R work R free
0.323 0.323 0.321
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Translation Termination and Ribosome Recycling in Eukaryotes.
Hellen CUT. (2018)
3 more

4 mentions without citation

Crystal Structure of the Human Ribosome in Complex with DENR-MCT-1.
Lomakin et al. (2017)
3 more