5NPM: 50S ribosomal protein L1

Crystal structure of mutant ribosomal protein TTHL1 lacking 8 N-terminal residues in complex with 80NT 23S RNA from thermus thermophilus. Determined by X-ray diffraction at 2.7 Å resolution. Released 16 May 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Thermus thermophilus
Chains: 2
Atoms: 3,340
Mol. weight: 49.81 kDa
Ligands: MLI
Released: 16 May 2018

Explore 5NPM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NPM contains 12 α-helices and 11 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	19-20	2	1
α-helix	22-32	11
α-helix	39	1
β-strand	40-47	8	1
α-helix	54-56	3
β-strand	59-63	5	2
β-strand	74-77	4	3
α-helix	81-88	8
β-strand	93-95	3	3
α-helix	97-99	3
α-helix	100-104	5
β-strand	112-115	4	3
α-helix	117-119	3
α-helix	120-131	12
α-helix	132-134	3
α-helix	140-142	3
β-strand	145	1	3
α-helix	149-157	9
β-strand	160-164	5	2
β-strand	170-177	8	1
α-helix	182-197	16
β-strand	209-216	8	1
β-strand	222-224	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
50S ribosomal protein L1	A	protein	220	Thermus thermophilus	Q5SLP7 (AlphaFold model)
23S ribosomal RNA	B	RNA	80	Thermus thermophilus

Sequence of entity 1 (A), FASTA

>5NPM_1 50S ribosomal protein L1 (chains A)
ALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGL
GKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLG
RILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADN
IRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Sequence of entity 2 (B), FASTA

>5NPM_2 23S ribosomal RNA (chains B)
GGGAUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCC
GGUGAAAUACCACCCUUCCC

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	1

Water and common crystallization additives (NA) are not listed.

Primary citation

[Influence of Nonconserved Regions of L1 Protuberance of Thermus thermophilus Ribosome on the Affinity of L1 Protein to 23s rRNA]. Kostareva, O.S., Nevskaya, N.A., Tishchenko, S.V. et al. Mol Biol (Mosk) (2018) 52:106-111. DOI 10.7868/S0026898418010147 · PubMed

Other PDB entries of the same protein (UniProt Q5SLP7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TG8 1.95 Å, Mutant ribosomal protein L1 lacking ala158 from thermus thermophilus
2OV7 2.3 Å, The first domain of the ribosomal protein L1 from Thermus thermophilus
2OUM 2.55 Å, The first domain of L1 from Thermus thermophilus
4U26 2.8 Å, Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.
4U27 2.8 Å, Crystal structure of the E. coli ribosome bound to flopristin and linopristin.
4V51 2.8 Å, Structure of the Thermus thermophilus 70S ribosome complexed with mRNA, tRNA and…
4WPO 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
4WQF 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
4WQU 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
4WQY 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
4V9H 2.86 Å, Crystal structure of the ribosome bound to elongation factor G in the guanosine…
4U20 2.9 Å, Crystal structure of the E. coli ribosome bound to flopristin.

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