8BIM: 50S ribosomal protein L2

Name: PDB 8BIM: Initiation complex of the E. coli 70S ribosome with mRNA containing AAm6A codon in the A-site
Published: 2023-08-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Initiation complex of the E. coli 70S ribosome with mRNA containing AAm6A codon in the A-site. Determined by electron microscopy at 2.04 Å resolution. Released 16 Aug 2023.

Method: Electron microscopy
Resolution: 2.04 Å
Organisms: Escherichia coli K-12, synthetic construct
Chains: 54
Atoms: 141,040
Mol. weight: 2174.26 kDa
Ligands: FME
Released: 16 Aug 2023

Explore 8BIM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BIM contains 243 α-helices and 299 β-strands across 49 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 a: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-17	8
β-strand	29-30	2	89
β-strand	37-38	2	89
β-strand	48-49	2	90
β-strand	52-53	2	90

Chain A: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
α-helix	6-7	2
β-strand	17-19	3	1
α-helix	28-30	3
α-helix	31-33	3
β-strand	34-36	3	2
β-strand	43	1	3
β-strand	49	1	3
β-strand	54	1	4
β-strand	61-63	3	2
β-strand	76-82	7	5
β-strand	91-96	6	5
β-strand	101-105	5	5
β-strand	107	1	6
β-strand	115-116	2	5
β-strand	118	1	7
β-strand	129-131	3	7
α-helix	132-134	3
β-strand	140-142	3	7
β-strand	144	1	8
β-strand	154	1	8
β-strand	162-168	7	7
β-strand	171-175	5	7
β-strand	181-185	5	7
β-strand	189-192	4	7
β-strand	195	1	6
α-helix	198-202	5
β-strand	204	1	1
α-helix	208-213	6
β-strand	216	1	4
α-helix	217-219	3
α-helix	222-224	3
β-strand	245	1	9
β-strand	251	1	9
α-helix	264-266	3
β-strand	267-269	3	7

Chain b: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	91
β-strand	20-25	6	91
α-helix	33-34	2
β-strand	35-40	6	91
β-strand	45-52	8	91

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	10
β-strand	21-28	8	10
β-strand	32-38	7	11
β-strand	47-51	5	11
α-helix	57-59	3
α-helix	62-71	10
β-strand	80-83	4	11
β-strand	95-96	2	11
α-helix	98-101	4
β-strand	106-112	7	10
β-strand	115-119	5	12
α-helix	121-125	5
α-helix	127-129	3
β-strand	163-166	4	12
β-strand	169-181	13	10
β-strand	186-190	5	10
β-strand	200-205	6	10

Chain c: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-22	5
α-helix	25-37	13

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	14
β-strand	11-13	3	14
α-helix	16-19	4
α-helix	25-37	13
α-helix	68-69	2
α-helix	98-115	18
β-strand	118-121	4	15
α-helix	131-141	11
β-strand	146-150	5	15
α-helix	155-161	7
β-strand	167-171	5	15
α-helix	177-182	6
β-strand	185-189	5	15
α-helix	190-200	11

Chain d: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	15-16	2	13
β-strand	22-24	3	13
α-helix	38-43	6
β-strand	48-49	2	13
α-helix	50-51	2
α-helix	52-61	10

Chain D: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	8-12	5
α-helix	13-20	8
α-helix	25-27	3
β-strand	31-39	9	17
α-helix	42-44	3
α-helix	48-61	14
α-helix	64-65	2
β-strand	66-69	4	17
β-strand	74	1	18
β-strand	79	1	18
β-strand	84-91	8	17
α-helix	94-102	9
α-helix	103-107	5
α-helix	108-110	3
β-strand	117	1	19
β-strand	122	1	17
β-strand	128-132	5	17
α-helix	135-137	3
β-strand	152-158	7	17
α-helix	163-171	9
β-strand	177	1	19

41 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
50S ribosomal protein L2	A	protein	273	Escherichia coli K-12	P60422 (AlphaFold model)
50S ribosomal protein L3	B	protein	209	Escherichia coli K-12	P60438 (AlphaFold model)
50S ribosomal protein L4	C	protein	201	Escherichia coli K-12	P60723 (AlphaFold model)
50S ribosomal protein L5	D	protein	179	Escherichia coli K-12	P62399 (AlphaFold model)
50S ribosomal protein L6	E	protein	177	Escherichia coli K-12	P0AG55
50S ribosomal protein L9	F	protein	149	Escherichia coli K-12	P0A7R1
50S ribosomal protein L13	G	protein	142	Escherichia coli K-12	P0AA10
50S ribosomal protein L14	H	protein	123	Escherichia coli K-12	P0ADY3
50S ribosomal protein L15	I	protein	144	Escherichia coli K-12	P02413
50S ribosomal protein L16	J	protein	136	Escherichia coli K-12	P0ADY7
50S ribosomal protein L17	K	protein	127	Escherichia coli K-12	P0AG44
50S ribosomal protein L18	L	protein	117	Escherichia coli K-12	P0C018

42 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8BIM_1 50S ribosomal protein L2 (chains A)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 2 (B), FASTA

>8BIM_2 50S ribosomal protein L3 (chains B)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 3 (C), FASTA

>8BIM_3 50S ribosomal protein L4 (chains C)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 4 (D), FASTA

>8BIM_4 50S ribosomal protein L5 (chains D)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Sequence of entity 5 (E), FASTA

>8BIM_5 50S ribosomal protein L6 (chains E)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 6 (F), FASTA

>8BIM_6 50S ribosomal protein L9 (chains F)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Sequence of entity 7 (G), FASTA

>8BIM_7 50S ribosomal protein L13 (chains G)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI

Sequence of entity 8 (H), FASTA

>8BIM_8 50S ribosomal protein L14 (chains H)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EVL

Sequence of entity 9 (I), FASTA

>8BIM_9 50S ribosomal protein L15 (chains I)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 10 (J), FASTA

>8BIM_10 50S ribosomal protein L16 (chains J)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM

Sequence of entity 11 (K), FASTA

>8BIM_11 50S ribosomal protein L17 (chains K)
MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSV
ANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSE
KAEAAAE

Sequence of entity 12 (L), FASTA

>8BIM_12 50S ribosomal protein L18 (chains L)
MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAE
QLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF

Ligands and cofactors

ID	Name	Formula	Copies
FME	N-formylmethionine	C6 H11 N O3 S	1

Primary citation

Modulation of translational decoding by m 6 A modification of mRNA. Jain, S., Koziej, L., Poulis, P. et al. Nat Commun (2023) 14:4784-4784. DOI 10.1038/s41467-023-40422-7 · PubMed

Other PDB entries of the same protein (UniProt P60422 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
8CGV 1.66 Å, Tiamulin bound to the 50S subunit
8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
8CAM 1.86 Å, Evernimicin bound to the 50S subunit
9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
8E30 1.91 Å, E. coli 50S ribosome bound to compound streptogramin A analog 3142

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