› 8xp3

Electron Microscopy
3.4Å resolution

Cryo-EM structure of the human 40S ribosome with LARP1 and LRRC47

Released:
DOI: 10.2210/pdb8xp3/pdb
PDB entry 8xp3 coloured by chain, front view.
PDB entry 8xp3 coloured by chain, side view.
PDB entry 8xp3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
LARP1 binds ribosomes and TOP mRNAs in repressed complexes.
Saba JA, Huang Z, Schole KL, Ye X, Bhatt SD, Li Y, Timp W, Cheng J, Green R
EMBO J (2024)
PMID: 39533057
Related structures: EMD-38549

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 domain:

Structure analysis Details

Assembly composition:
hetero 37-mer (preferred)
PDBe Complex ID:
PDB-CPX-293720 (preferred)
Entry contents:
36 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (37 distinct):
Small ribosomal subunit protein eS32 Chain: Ln
Molecule details ›
Chain: Ln
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
Small ribosomal subunit protein uS2 Chain: SA
Molecule details ›
Chain: SA
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 Chain: SB
Small ribosomal subunit protein uS3 Chain: SD
Small ribosomal subunit protein eS4, X isoform Chain: SE
Small ribosomal subunit protein uS7 Chain: SF
Small ribosomal subunit protein eS7 Chain: SH
Small ribosomal subunit protein eS8 Chain: SI
Small ribosomal subunit protein eS10 Chain: SK
Small ribosomal subunit protein uS17 Chain: SL
Small ribosomal subunit protein uS19 Chain: SP
Small ribosomal subunit protein uS9 Chain: SQ
Small ribosomal subunit protein eS17 Chain: SR
Small ribosomal subunit protein uS13 Chain: SS
Small ribosomal subunit protein eS19 Chain: ST
Small ribosomal subunit protein uS10 Chain: SU
Small ribosomal subunit protein eS21 Chain: SV
Small ribosomal subunit protein uS12 Chain: SX
Small ribosomal subunit protein eS26 Chain: Sa
Small ribosomal subunit protein eS28 Chain: Sc
Small ribosomal subunit protein uS14 Chain: Sd
Small ribosomal subunit protein RACK1 Chain: Sg
Small ribosomal subunit protein uS5 Chain: SC
Small ribosomal subunit protein eS6 Chain: SG
Small ribosomal subunit protein uS4 Chain: SJ
Small ribosomal subunit protein eS12 Chain: SM
Small ribosomal subunit protein uS15 Chain: SN
Small ribosomal subunit protein uS11 Chain: SO
Small ribosomal subunit protein uS8 Chain: SW
Small ribosomal subunit protein eS24 Chain: SY
Small ribosomal subunit protein eS25 Chain: SZ
Small ribosomal subunit protein eS27 Chain: Sb
Small ribosomal subunit protein eS30 Chain: Se
Ubiquitin-ribosomal protein eS31 fusion protein Chain: Sf
La-related protein 1 Chain: JD
Leucine-rich repeat-containing protein 47 Chain: JC
18S Ribosomal RNA Chain: S2

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.4Å
Relevant EMDB volumes: EMD-38549

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