8R6C: Large ribosomal subunit protein bL33

Name: PDB 8R6C: 70S Escherichia coli ribosome with Paenilamicin B2 bound with A- and P-site tRNA.
Published: 2024-07-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

70S Escherichia coli ribosome with Paenilamicin B2 bound with A- and P-site tRNA. Determined by electron microscopy at 2.2 Å resolution. Released 24 Jul 2024.

Method: Electron microscopy
Resolution: 2.2 Å
Organisms: Escherichia coli BW25113, synthetic construct
Chains: 57
Atoms: 145,010
Mol. weight: 2226.54 kDa
Ligands: MG, ZN
Released: 24 Jul 2024

Explore 8R6C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R6C contains 262 α-helices and 306 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: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
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	15-16	2	4
β-strand	22-24	3	4
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	4
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	6
β-strand	14-18	5	6
β-strand	23-27	5	6
α-helix	31-33	3
β-strand	35-37	3	6

Chain 4: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-13	4	9
β-strand	14-16	3	10
β-strand	23-26	4	9
β-strand	32-34	3	10
α-helix	42-45	4
α-helix	56-64	9

Chain 6: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	20
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-34	4	20
β-strand	38-41	4	20
α-helix	43-62	20
β-strand	67-70	4	21
α-helix	76-86	11
β-strand	90-92	3	21
α-helix	96-97	2
α-helix	104-123	20
α-helix	132-148	17
β-strand	160-164	5	21
α-helix	170-178	9
β-strand	183-187	5	21
β-strand	198-201	4	21
α-helix	207-226	20

Chain c: 8 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	11
α-helix	6-7	2
β-strand	17-19	3	11
α-helix	31-33	3
β-strand	34-36	3	12
β-strand	43	1	13
β-strand	49	1	13
β-strand	54	1	14
β-strand	61-63	3	12
β-strand	65	1	15
β-strand	76-82	7	15
β-strand	91-96	6	15
β-strand	101-105	5	15
β-strand	107	1	16
β-strand	115-116	2	15
β-strand	118	1	17
β-strand	129-131	3	17
α-helix	136	1
β-strand	140-142	3	17
β-strand	144-145	2	18
β-strand	152-154	3	18
β-strand	162-168	7	17
β-strand	171-175	5	17
β-strand	181-185	5	17
β-strand	189-192	4	17
β-strand	195	1	16
α-helix	198-202	5
β-strand	204	1	11
α-helix	208-213	6
β-strand	216	1	14
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	19
β-strand	251	1	19
α-helix	264-266	3
β-strand	267-269	3	17

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
Large ribosomal subunit protein bL33	0	protein	55	Escherichia coli BW25113	P0A7N9 (AlphaFold model)
Large ribosomal subunit protein bL34	1	protein	46	Escherichia coli BW25113	P0A7P5 (AlphaFold model)
Large ribosomal subunit protein bL35	2	protein	65	Escherichia coli BW25113	P0A7Q1 (AlphaFold model)
Large ribosomal subunit protein bL36A	3	protein	38	Escherichia coli BW25113	P0A7Q6 (AlphaFold model)
Large ribosomal subunit protein bL31A	4	protein	70	Escherichia coli BW25113	P0A7M9
N-Formylmethionine tRNA	5	RNA	77	Escherichia coli BW25113
16S ribosomal RNA	A	RNA	1534	Escherichia coli BW25113
30S ribosomal protein S2	B	protein	241	Escherichia coli BW25113	P0A7V0
Small ribosomal subunit protein uS3	C	protein	233	Escherichia coli BW25113	P0A7V3
Small ribosomal subunit protein uS4	D	protein	206	Escherichia coli BW25113	P0A7V8
Small ribosomal subunit protein uS5	E	protein	167	Escherichia coli BW25113	P0A7W1
30S ribosomal protein S6, fully modified isoform	F	protein	135	Escherichia coli BW25113	P02358

45 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8R6C_1 Large ribosomal subunit protein bL33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>8R6C_2 Large ribosomal subunit protein bL34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>8R6C_3 Large ribosomal subunit protein bL35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>8R6C_4 Large ribosomal subunit protein bL36A (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (4), FASTA

>8R6C_5 Large ribosomal subunit protein bL31A (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIPGSK

Sequence of entity 6 (5), FASTA

>8R6C_6 N-Formylmethionine tRNA (chains 5)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA

Sequence of entity 7 (A), FASTA

>8R6C_7 16S ribosomal RNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
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 8 (B), FASTA

>8R6C_8 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 9 (C), FASTA

>8R6C_9 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 10 (D), FASTA

>8R6C_10 Small ribosomal subunit protein uS4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 11 (E), FASTA

>8R6C_11 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 12 (F), FASTA

>8R6C_12 30S ribosomal protein S6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	308
ZN	Zinc ion	Zn	2

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

Primary citation

Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis. Koller, T.O., Berger, M.J., Morici, M. et al. bioRxiv (2024). DOI 10.1101/2024.05.21.595107 · 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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