8EMM: 50S ribosomal protein L2

Name: PDB 8EMM: Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates
Published: 2023-05-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates. Determined by electron microscopy at 2.1 Å resolution. Released 31 May 2023.

Method: Electron microscopy
Resolution: 2.1 Å
Organism: Escherichia coli
Chains: 55
Atoms: 145,735
Mol. weight: 2210.53 kDa
Ligands: PAR, MET, ZN, SPM
Released: 31 May 2023

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

Secondary structure: helices and β-sheets

8EMM contains 258 α-helices and 298 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 0: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	1
β-strand	20-25	6	1
α-helix	33-34	2
β-strand	35-40	6	1
β-strand	45-52	8	1

Chain 1: 3 helices, 0 β-strands

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

Chain 2: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	11
β-strand	22-25	4	11
α-helix	26	1
α-helix	38-44	7
β-strand	47-49	3	11
α-helix	50-51	2
α-helix	52-54	3
α-helix	55-61	7

Chain 3: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	16
β-strand	14-19	6	16
β-strand	22-27	6	16
α-helix	31-33	3
β-strand	35-37	3	16

Chain 4: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-11	2	19
β-strand	14-16	3	20
β-strand	22	1	20
β-strand	25-26	2	19
β-strand	32-34	3	20
α-helix	56-63	8

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	32
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-34	4	32
β-strand	38-41	4	32
α-helix	43-62	20
β-strand	67-70	4	33
α-helix	77-85	9
β-strand	90-92	3	33
α-helix	96-97	2
α-helix	104-121	18
α-helix	133-148	16
β-strand	160-164	5	33
α-helix	170-179	10
β-strand	183-187	5	33
β-strand	198-201	4	33
α-helix	207-226	20

Chain c: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	2
α-helix	6-7	2
β-strand	17-19	3	2
β-strand	24	1	3
α-helix	31-33	3
β-strand	34-35	2	4
β-strand	43	1	5
β-strand	49	1	5
β-strand	54	1	6
α-helix	61	1
β-strand	62-63	2	4
β-strand	65	1	3
β-strand	72	1	7
β-strand	76-82	7	3
β-strand	91-96	6	3
β-strand	101-105	5	3
β-strand	107	1	8
β-strand	115-116	2	3
β-strand	118	1	7
β-strand	129-131	3	7
α-helix	136	1
β-strand	140-142	3	7
β-strand	144-145	2	9
β-strand	152-154	3	9
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	8
α-helix	198-202	5
β-strand	204	1	2
α-helix	208-212	5
β-strand	216	1	6
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	10
β-strand	251	1	10
α-helix	264-266	3
β-strand	267-269	3	7

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	20	1	39
α-helix	26-46	21
β-strand	52-58	7	39
β-strand	64-70	7	39
α-helix	73-77	5
α-helix	82-95	14
β-strand	99-105	7	39
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-155	8	40
α-helix	157-159	3
β-strand	164-171	8	40
β-strand	182-191	10	40
β-strand	194-203	10	40

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
23S rRNA	a	RNA	2904	Escherichia coli
5S rRNA	b	RNA	120	Escherichia coli
50S ribosomal protein L2	c	protein	273	Escherichia coli	P60422 (AlphaFold model)
50S ribosomal protein L3	d	protein	209	Escherichia coli	P60438 (AlphaFold model)
50S ribosomal protein L4	e	protein	201	Escherichia coli	P60723 (AlphaFold model)
50S ribosomal protein L5	f	protein	179	Escherichia coli	P62399 (AlphaFold model)
50S ribosomal protein L6	g	protein	177	Escherichia coli	P0AG55
50S ribosomal protein L9	h	protein	149	Escherichia coli	P0A7R1
50S ribosomal protein L13	i	protein	142	Escherichia coli	P0AA10
50S ribosomal protein L14	j	protein	123	Escherichia coli	P0ADY3
50S ribosomal protein L15	k	protein	144	Escherichia coli	P02413
50S ribosomal protein L16	l	protein	136	Escherichia coli	P0ADY7

42 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>8EMM_1 23S rRNA (chains a)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCUU

Sequence of entity 2 (b), FASTA

>8EMM_2 5S rRNA (chains b)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU

Sequence of entity 3 (c), FASTA

>8EMM_3 50S ribosomal protein L2 (chains c)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 4 (d), FASTA

>8EMM_4 50S ribosomal protein L3 (chains d)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 5 (e), FASTA

>8EMM_5 50S ribosomal protein L4 (chains e)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 6 (f), FASTA

>8EMM_6 50S ribosomal protein L5 (chains f)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Sequence of entity 7 (g), FASTA

>8EMM_7 50S ribosomal protein L6 (chains g)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 8 (h), FASTA

>8EMM_8 50S ribosomal protein L9 (chains h)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Sequence of entity 9 (i), FASTA

>8EMM_9 50S ribosomal protein L13 (chains i)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI

Sequence of entity 10 (j), FASTA

>8EMM_10 50S ribosomal protein L14 (chains j)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EVL

Sequence of entity 11 (k), FASTA

>8EMM_11 50S ribosomal protein L15 (chains k)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 12 (l), FASTA

>8EMM_12 50S ribosomal protein L16 (chains l)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVXXGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM

Ligands and cofactors

ID	Name	Formula	Copies
PAR	Paromomycin	C23 H45 N5 O14	1
MET	Methionine	C5 H11 N O2 S	2
ZN	Zinc ion	Zn	2
SPM	Spermine	C10 H26 N4	1
SPD	Spermidine	C7 H19 N3	17
MG	Magnesium ion	Mg	321

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

Primary citation

Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates. Watson, Z.L., Knudson, I.J., Ward, F.R. et al. Nat Chem (2023) 15:913-921. DOI 10.1038/s41557-023-01226-w · 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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