9SLG: Large ribosomal subunit protein bL33

Name: PDB 9SLG: Doxycycline Bound E. coli Ribosome with Rearranged Peptidyl Transferase Centre
Published: 2026-04-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Doxycycline Bound E. coli Ribosome with Rearranged Peptidyl Transferase Centre. Determined by electron microscopy at 2.16 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 2.16 Å
Organism: Escherichia coli BL21(DE3)
Chains: 54
Atoms: 150,218
Mol. weight: 2187.81 kDa
Ligands: DXT, MG, ZN
Released: 22 Apr 2026

Explore 9SLG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9SLG contains 281 α-helices and 315 β-strands across 51 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: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	6
β-strand	22-24	3	6
α-helix	25-26	2
α-helix	38-43	6
β-strand	48-49	2	6
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	15
β-strand	14-19	6	15
β-strand	22-27	6	15
α-helix	31-33	3
β-strand	35-37	3	15

Chain 4: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-16	7	19
β-strand	21-26	6	19
β-strand	32-34	3	19
α-helix	42-45	4
α-helix	56-63	8

Chain 6: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	23-32	10
β-strand	41	1	2
β-strand	43-48	6	3
β-strand	60-64	5	4
β-strand	160-164	5	4
β-strand	170-171	2	3
β-strand	177	1	2
α-helix	182-198	17
β-strand	209-215	7	3
α-helix	220-221	2
β-strand	222-223	2	3

Chain B: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	16-19	4	27
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-35	5	27
β-strand	38-41	4	27
α-helix	43-61	19
β-strand	67-70	4	28
α-helix	74-85	12
β-strand	90-92	3	28
α-helix	96-97	2
α-helix	104-122	19
α-helix	125-128	4
α-helix	131-148	18
β-strand	160-163	4	28
α-helix	170-179	10
β-strand	183-187	5	28
β-strand	198-201	4	28
α-helix	207-226	20

Chain c: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	7
α-helix	6-7	2
β-strand	17-19	3	7
β-strand	24	1	8
α-helix	31-33	3
β-strand	34-36	3	9
β-strand	43	1	10
β-strand	49	1	10
β-strand	61-63	3	9
β-strand	65	1	8
β-strand	76-82	7	8
β-strand	91-96	6	8
β-strand	101-105	5	8
β-strand	107	1	11
β-strand	115-116	2	8
β-strand	118	1	12
β-strand	129-131	3	12
α-helix	132-134	3
α-helix	136	1
β-strand	140-142	3	12
β-strand	144-145	2	13
β-strand	152-154	3	13
β-strand	162-168	7	12
β-strand	171-175	5	12
β-strand	181-185	5	12
β-strand	189-192	4	12
β-strand	195	1	11
α-helix	198-202	5
β-strand	204	1	7
α-helix	208-212	5
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	14
β-strand	251	1	14
α-helix	264-266	3
β-strand	267-269	3	12

43 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
Large ribosomal subunit protein bL33	0	protein	55	Escherichia coli BL21(DE3)	P0A7N9 (AlphaFold model)
Large ribosomal subunit protein bL34	1	protein	46	Escherichia coli BL21(DE3)	P0A7P5 (AlphaFold model)
Large ribosomal subunit protein bL35	2	protein	65	Escherichia coli BL21(DE3)	P0A7Q1 (AlphaFold model)
Large ribosomal subunit protein bL36A	3	protein	38	Escherichia coli BL21(DE3)	P0A7Q6 (AlphaFold model)
Large ribosomal subunit protein bL31	4	protein	67	Escherichia coli BL21(DE3)	P0A7M9
16S ribosomal RNA	A	RNA	1534	Escherichia coli BL21(DE3)
Small ribosomal subunit protein uS2	B	protein	241	Escherichia coli BL21(DE3)	P0A7V0
Small ribosomal subunit protein uS3	C	protein	233	Escherichia coli BL21(DE3)	P0A7V3
Small ribosomal subunit protein uS4	D	protein	206	Escherichia coli BL21(DE3)	P0A7V8
Small ribosomal subunit protein uS5	E	protein	167	Escherichia coli BL21(DE3)	P0A7W1
Small ribosomal subunit protein bS6	F	protein	131	Escherichia coli BL21(DE3)	P02358
Small ribosomal subunit protein uS7	G	protein	156	Escherichia coli BL21(DE3)	P02359

42 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>9SLG_1 Large ribosomal subunit protein bL33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>9SLG_2 Large ribosomal subunit protein bL34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>9SLG_3 Large ribosomal subunit protein bL35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>9SLG_4 Large ribosomal subunit protein bL36A (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (4), FASTA

>9SLG_5 Large ribosomal subunit protein bL31 (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIP

Sequence of entity 6 (A), FASTA

>9SLG_6 16S ribosomal RNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGCAGCUUGCUGCUUCGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA

Sequence of entity 7 (B), FASTA

>9SLG_7 Small ribosomal subunit protein uS2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 8 (C), FASTA

>9SLG_8 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 9 (D), FASTA

>9SLG_9 Small ribosomal subunit protein uS4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 10 (E), FASTA

>9SLG_10 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPAMVAAKRGKSVEEILGK

Sequence of entity 11 (F), FASTA

>9SLG_11 Small ribosomal subunit protein bS6 (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDADAGDSEE

Sequence of entity 12 (G), FASTA

>9SLG_12 Small ribosomal subunit protein uS7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW

Ligands and cofactors

ID	Name	Formula	Copies
DXT	(4S,4AR,5S,5AR,6R,12AS)-4-(dimethylamino)-3,5,10,12,12A-pentahydroxy-6-methyl-1…	C22 H24 N2 O8	1
MG	Magnesium ion	Mg	447
ZN	Zinc ion	Zn	2

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

Primary citation

To be confirmed, Doxycycline Bound 50S E. coli Ribosome with Rearranged Peptidyl Transferase Centre. Stuart, W.S., Isupov, M.N., McLaren, M. et al. To be published.

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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