487D: 50S ribosomal protein L1

Seven ribosomal proteins fitted to a CRYO-electron microscopic map of the large 50S subunit at 7.5 Å resolution. Determined by electron microscopy at 7.5 Å resolution. Released 10 Apr 2000.

Method: Electron microscopy
Resolution: 7.5 Å
Organisms: Thermus thermophilus, Geobacillus stearothermophilus, Thermotoga maritima
Chains: 7
Atoms: 7,825
Mol. weight: 111.62 kDa
Released: 10 Apr 2000

Explore 487D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

487D contains 36 α-helices and 73 β-strands across 7 chains. 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 H: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	1
α-helix	22-30	9
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	120-134	15
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	209-215	7	1
β-strand	222-224	3	1

Chain I: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	61-63	3
β-strand	64	1	4
β-strand	75-83	9	4
β-strand	88-95	8	4
β-strand	100-104	5	4
β-strand	114-115	2	4
β-strand	117	1	5
β-strand	128-130	3	5
α-helix	131-133	3
β-strand	139-141	3	5
β-strand	143-144	2	6
β-strand	151-153	3	6
β-strand	161-162	2	5
β-strand	163-167	5	7
β-strand	170-174	5	7
β-strand	180-184	5	7
β-strand	188-191	4	5

Chain J: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	8
β-strand	15-19	5	9
β-strand	22-27	6	9
β-strand	30-35	6	9
β-strand	41-45	5	8
β-strand	48-52	5	8
α-helix	58-79	22
β-strand	83-89	7	10
β-strand	94-98	5	11
β-strand	101-105	5	11
β-strand	112-114	3	11
β-strand	120-126	7	10
β-strand	129-134	6	10
α-helix	137-148	12
α-helix	152-154	3
β-strand	160-163	4	10

Chain K: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	12
β-strand	8-9	2	13
β-strand	11-12	2	13
α-helix	13-15	3
β-strand	18-20	3	12
α-helix	21-22	2
α-helix	25	1
α-helix	26-30	5
β-strand	36-38	3	12
α-helix	41-72	32
β-strand	77-81	5	14
β-strand	83	1	15
α-helix	85-87	3
β-strand	88-93	6	16
α-helix	95-106	12
α-helix	112-114	3
β-strand	115	1	14
α-helix	120	1
β-strand	121-123	3	16
β-strand	125-134	10	14
β-strand	137-147	11	14

Chain L: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	17
α-helix	25-29	5
α-helix	36-46	11
β-strand	54-59	6	17
β-strand	67-70	4	17
α-helix	72-74	3
α-helix	75-83	9
β-strand	98-100	3	18
α-helix	102-112	11
α-helix	113-115	3
α-helix	121-132	12
β-strand	137-139	3	18

Chain M: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	19
β-strand	7-10	4	20
β-strand	16-24	9	20
β-strand	33	1	19
β-strand	38-46	9	20
β-strand	57-64	8	20
β-strand	69-70	2	21
β-strand	76-77	2	21
β-strand	83-86	4	20
β-strand	102	1	22
α-helix	105-108	4
α-helix	112-117	6
β-strand	121	1	22

Chain N: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	23
α-helix	15-22	8
β-strand	25-31	7	23
β-strand	38-43	6	23
α-helix	44-52	9
α-helix	55-58	4
β-strand	61-65	5	23
β-strand	68-79	12	23
β-strand	86-93	8	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
50S ribosomal protein L1	H	protein	224	Thermus thermophilus	Q5SLP7 (AlphaFold model)
50S ribosomal protein L2	I	protein	135	Geobacillus stearothermophilus	P04257 (AlphaFold model)
50S ribosomal protein L6	J	protein	164	Geobacillus stearothermophilus	P02391 (AlphaFold model)
50S ribosomal protein L9	K	protein	149	Geobacillus stearothermophilus	P02417 (AlphaFold model)
50S ribosomal protein L11	L	protein	133	Thermotoga maritima	P29395
50S ribosomal protein L14	M	protein	122	Geobacillus stearothermophilus	P04450
50S ribosomal protein L25	N	protein	94	Escherichia coli	P68919

Sequence of entity 1 (H), FASTA

>487D_1 50S ribosomal protein L1 (chains H)
KRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSL
PHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVG
SKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEK
LADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Sequence of entity 2 (I), FASTA

>487D_2 50S ribosomal protein L2 (chains I)
QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGP
DADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGE
VRMILGKCRATVGEV

Sequence of entity 3 (J), FASTA

>487D_3 50S ribosomal protein L6 (chains J)
PIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHHRALHGT
TRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGLEIEVPS
QTKIIVKGADKQRVGELAANIRAVRPPEPYKGKGIRYEGELVRL

Sequence of entity 4 (K), FASTA

>487D_4 50S ribosomal protein L9 (chains K)
MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAE
ELANAKKLKEQLEKLTVTIPAKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELADA
IRALGYTNVPVKLHPEVTATLKVHVTEQK

Sequence of entity 5 (L), FASTA

>487D_5 50S ribosomal protein L11 (chains L)
QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFT
FIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKI
IEGTAKSMGIEVV

Sequence of entity 6 (M), FASTA

>487D_6 50S ribosomal protein L14 (chains M)
MIQQESRLKVADNSGAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVKKGQVVKA
VVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELRDKDFMKIISLAPE
VI

Sequence of entity 7 (N), FASTA

>487D_7 50S ribosomal protein L25 (chains N)
MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEV
LTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

Primary citation

The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution. Mueller, F., Sommer, I., Baranov, P. et al. J Mol Biol (2000) 298:35-59. DOI 10.1006/jmbi.2000.3635 · 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
5NPM 2.7 Å, Crystal structure of mutant ribosomal protein TTHL1 lacking 8 N-terminal residues in…
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…

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