9GHB: 50S ribosomal protein L33

Name: PDB 9GHB: Fusidic acid-locked Escherichia coli 70S ribosome with Staphylococcus aureus EF-G in post-translocational state (POST)
Published: 2025-03-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Fusidic acid-locked Escherichia coli 70S ribosome with Staphylococcus aureus EF-G in post-translocational state (POST). Determined by electron microscopy at 2.21 Å resolution. Released 26 Mar 2025.

Method: Electron microscopy
Resolution: 2.21 Å
Organisms: Escherichia coli K-12, Staphylococcus aureus subsp. aureus NCTC 8325
Chains: 55
Atoms: 145,490
Mol. weight: 2274.68 kDa
Ligands: ZN, MG, GDP, FUA
Released: 26 Mar 2025

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

Secondary structure: helices and β-sheets

9GHB contains 270 α-helices and 343 β-strands across 50 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	18-23	6
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	15-16	2	13
β-strand	22-24	3	13
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	13
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	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, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	17
β-strand	22-26	5	17
β-strand	32-34	3	17
α-helix	42-45	4
α-helix	56-63	8

Chain B: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	31
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-35	5	31
β-strand	38-41	4	31
α-helix	43-62	20
α-helix	65-66	2
β-strand	67-70	4	32
α-helix	74-86	13
β-strand	90-92	3	32
α-helix	104-123	20
α-helix	125-128	4
α-helix	132-148	17
β-strand	160-164	5	32
α-helix	170-179	10
β-strand	183-187	5	32
β-strand	198-201	4	32
α-helix	207-225	19

Chain c: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	18
α-helix	6-7	2
β-strand	17-19	3	18
β-strand	24	1	19
α-helix	31-33	3
β-strand	34-36	3	20
β-strand	43	1	21
β-strand	49	1	21
β-strand	54	1	22
β-strand	61-63	3	20
β-strand	65	1	19
β-strand	72	1	23
β-strand	76-82	7	19
β-strand	91-96	6	19
β-strand	101-105	5	19
β-strand	107	1	24
β-strand	115-116	2	19
β-strand	118	1	23
β-strand	129-131	3	23
α-helix	136	1
β-strand	140-142	3	23
β-strand	144-145	2	25
β-strand	152-154	3	25
β-strand	162-168	7	23
β-strand	171-175	5	23
β-strand	181-185	5	23
β-strand	189-192	4	23
β-strand	195	1	24
α-helix	198-202	5
β-strand	204	1	18
α-helix	208-213	6
β-strand	216	1	22
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	26
β-strand	251	1	26
α-helix	264-266	3
β-strand	267-269	3	23

Chain C: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	12	1	35
β-strand	16	1	35
β-strand	20	1	36
α-helix	26-46	21
α-helix	48-50	3
β-strand	52-58	7	36
β-strand	64-70	7	36
α-helix	73-77	5
α-helix	79-81	3
α-helix	82-95	14
β-strand	99-105	7	36
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-155	8	37
β-strand	164-171	8	37
β-strand	180-190	11	37
β-strand	195-206	12	37

42 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 K-12	P0A7N9 (AlphaFold model)
50S ribosomal protein L34	1	protein	46	Escherichia coli K-12	P0A7P5 (AlphaFold model)
50S ribosomal protein L35	2	protein	65	Escherichia coli K-12	P0A7Q1 (AlphaFold model)
50S ribosomal protein L36	3	protein	38	Escherichia coli K-12	P0A7Q6 (AlphaFold model)
50S ribosomal protein L31	4	protein	70	Escherichia coli K-12	P0A7M9
mRNA	9	RNA	24	Escherichia coli K-12
16S rRNA	A	RNA	1554	Escherichia coli K-12
30S ribosomal protein S2	B	protein	241	Escherichia coli K-12	P0A7V0
30S ribosomal protein S3	C	protein	233	Escherichia coli K-12	P0A7V3
30S ribosomal protein S4	D	protein	206	Escherichia coli K-12	P0A7V8
30S ribosomal protein S5	E	protein	167	Escherichia coli K-12	P0A7W1
30S ribosomal protein S6	F	protein	135	Escherichia coli K-12	P02358

43 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>9GHB_1 50S ribosomal protein L33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>9GHB_2 50S ribosomal protein L34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>9GHB_3 50S ribosomal protein L35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>9GHB_4 50S ribosomal protein L36 (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (4), FASTA

>9GHB_5 50S ribosomal protein L31 (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIPGSK

Sequence of entity 6 (9), FASTA

>9GHB_6 mRNA (chains 9)
GGCAAGGAGGUAAAAAUGGCAAAA

Sequence of entity 7 (A), FASTA

>9GHB_7 16S rRNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGCCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUACCUUAAAGAAGC

Sequence of entity 8 (B), FASTA

>9GHB_8 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 9 (C), FASTA

>9GHB_9 30S ribosomal protein S3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 10 (D), FASTA

>9GHB_10 30S ribosomal protein S4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 11 (E), FASTA

>9GHB_11 30S ribosomal protein S5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 12 (F), FASTA

>9GHB_12 30S ribosomal protein S6 (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	303
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
FUA	Fusidic acid	C31 H48 O6	1

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

Primary citation

Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis. Gonzalez-Lopez, A., Ge, X., Larsson, D.S.D. et al. Nat Commun (2025) 16:3693-3693. DOI 10.1038/s41467-025-58902-3 · 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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