8G6Y: WT E.coli ribosome 50S subunit with

Name: PDB 8G6Y: Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site 3-aminopyridine-4-carboxylic acid charged NH-tRNAPhe
Published: 2023-04-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site 3-aminopyridine-4-carboxylic acid charged NH-tRNAPhe. Determined by electron microscopy at 2.09 Å resolution. Released 5 Apr 2023.

Method: Electron microscopy
Resolution: 2.09 Å
Organism: Escherichia coli
Chains: 34
Atoms: 93,683
Mol. weight: 1415.82 kDa
Ligands: MG, FME, 8AN, YRW
Released: 5 Apr 2023

Explore 8G6Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G6Y contains 136 α-helices and 202 β-strands across 29 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	45-53	9	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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	14-16	3	8
β-strand	22-24	3	8
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	8
α-helix	50-51	2
α-helix	52-61	10

Chain 3: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	10
β-strand	14-19	6	10
β-strand	22-27	6	10
α-helix	31-33	3
β-strand	35-37	3	10

Chain 4: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	13
β-strand	21-26	6	13
β-strand	32-33	2	13
α-helix	38-40	3
α-helix	42-45	4
α-helix	56-63	8

Chain c: 9 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	19
α-helix	6-7	2
β-strand	17-19	3	19
β-strand	24	1	20
α-helix	31-33	3
β-strand	34-36	3	21
β-strand	43	1	22
β-strand	49	1	22
β-strand	54	1	23
β-strand	61-63	3	21
β-strand	65	1	20
β-strand	76-82	7	20
β-strand	91-96	6	20
β-strand	101-105	5	20
α-helix	106	1
β-strand	107	1	24
β-strand	115-116	2	20
β-strand	118	1	25
β-strand	129-131	3	25
α-helix	136	1
β-strand	140-142	3	25
β-strand	144-145	2	26
β-strand	152-154	3	26
β-strand	162-168	7	25
β-strand	171-175	5	25
β-strand	181-185	5	25
β-strand	189-192	4	25
β-strand	195	1	24
α-helix	198-202	5
β-strand	204	1	19
α-helix	208-213	6
β-strand	216	1	23
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	27
β-strand	251	1	27
α-helix	264-266	3
β-strand	267-269	3	25

Chain d: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	28
β-strand	21-28	8	28
β-strand	32-38	7	29
β-strand	47-51	5	29
α-helix	57-59	3
α-helix	62-71	10
β-strand	79-83	5	29
α-helix	84-85	2
β-strand	95-96	2	29
α-helix	98-101	4
β-strand	106-112	7	28
α-helix	113-114	2
β-strand	115-119	5	30
α-helix	121-125	5
α-helix	127-129	3
β-strand	149	1	31
β-strand	152	1	31
α-helix	155-156	2
β-strand	163-166	4	30
β-strand	169-181	13	28
β-strand	186-190	5	28
β-strand	200-205	6	28

Chain e: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	32
β-strand	5	1	33
β-strand	11-13	3	32
α-helix	16-19	4
α-helix	25-38	14
α-helix	68-69	2
α-helix	98-115	18
β-strand	118-121	4	33
α-helix	131-141	11
β-strand	146-150	5	33
α-helix	155-162	8
β-strand	167-171	5	33
α-helix	172-174	3
α-helix	177-182	6
β-strand	185-189	5	33
α-helix	190-199	10

21 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 L33	0	protein	55	Escherichia coli	P0A7N9 (AlphaFold model)
50S ribosomal protein L34	1	protein	46	Escherichia coli	P0A7P5 (AlphaFold model)
50S ribosomal protein L35	2	protein	65	Escherichia coli	P0A7Q1 (AlphaFold model)
50S ribosomal protein L36	3	protein	38	Escherichia coli	P0A7Q6 (AlphaFold model)
50S ribosomal protein L31	4	protein	70	Escherichia coli	P0A7M9
mRNA	X	RNA	28	Escherichia coli
A-site tRNA Phe	Y	RNA	76	Escherichia coli
P-site tRNA fMet	Z	RNA	76	Escherichia coli
23S rRNA	a	RNA	2904	Escherichia coli
5S rRNA	b	RNA	120	Escherichia coli
50S ribosomal protein L2	c	protein	273	Escherichia coli	P60422
50S ribosomal protein L3	d	protein	209	Escherichia coli	P60438

22 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8G6Y_1 50S ribosomal protein L33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>8G6Y_2 50S ribosomal protein L34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>8G6Y_3 50S ribosomal protein L35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>8G6Y_4 50S ribosomal protein L36 (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (4), FASTA

>8G6Y_5 50S ribosomal protein L31 (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIPGSK

Sequence of entity 6 (X), FASTA

>8G6Y_6 mRNA (chains X)
GUAUAAGGAGGUAAAAAUGUUCUAACUA

Sequence of entity 7 (Y), FASTA

>8G6Y_7 A-site tRNA Phe (chains Y)
GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUU
CCGAGUCCGGGCACCA

Sequence of entity 8 (Z), FASTA

>8G6Y_8 P-site tRNA fMet (chains Z)
GGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACC

Sequence of entity 9 (a), FASTA

>8G6Y_9 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 10 (b), FASTA

>8G6Y_10 5S rRNA (chains b)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU

Sequence of entity 11 (c), FASTA

>8G6Y_11 50S ribosomal protein L2 (chains c)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 12 (d), FASTA

>8G6Y_12 50S ribosomal protein L3 (chains d)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	231
FME	N-formylmethionine	C6 H11 N O3 S	1
8AN	3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)	C10 H15 N6 O6 P	1
YRW	3-aminopyridine-4-carboxamide	C6 H7 N3 O	1
ZN	Zinc ion	Zn	2

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

Primary citation

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome. Majumdar, C., Walker, J.A., Francis, M.B. et al. ACS Cent Sci (2023) 9:1160-1169. DOI 10.1021/acscentsci.3c00153 · PubMed

Other PDB entries of the same protein (UniProt P0A7N9 (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
9D89 1.95 Å, E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)

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