8BUU: ARE-ABCF VmlR2

Name: PDB 8BUU: ARE-ABCF VmlR2 bound to a 70S ribosome
Published: 2023-04-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

ARE-ABCF VmlR2 bound to a 70S ribosome. Determined by electron microscopy at 2.9 Å resolution. Released 5 Apr 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Bacillus subtilis subsp. subtilis str. 168, Neobacillus vireti
Chains: 51
Atoms: 144,765
Mol. weight: 2207.15 kDa
Ligands: MG, ATP, ZN
Released: 5 Apr 2023

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

Secondary structure: helices and β-sheets

8BUU contains 266 α-helices and 312 β-strands across 46 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: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	22-25	4
β-strand	27-29	3	1
β-strand	36-38	3	1
β-strand	41	1	48
β-strand	49	1	2
β-strand	52	1	2

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	3
β-strand	15-22	8	3
β-strand	31-36	6	3
β-strand	41-47	7	3

Chain 2: 3 helices, 0 β-strands

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

Chain 3: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	16
β-strand	22-24	3	16
α-helix	33-35	3
α-helix	38-44	7
β-strand	48-49	2	16
α-helix	52-58	7
α-helix	59-62	4

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	18
β-strand	15-18	4	18
β-strand	23-26	4	18
α-helix	30-32	3
β-strand	34-36	3	18

Chain 9: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	92
β-strand	21-32	12	92
β-strand	36-40	5	93
α-helix	47-55	9
β-strand	62-67	6	92
β-strand	73-75	3	93
α-helix	80-85	6
α-helix	87-93	7
α-helix	96-106	11
α-helix	111-113	3
α-helix	116-121	6
α-helix	124-137	14
β-strand	142-146	5	93
α-helix	154-166	13
β-strand	171-174	4	93
α-helix	178-184	7
β-strand	187-192	6	93
β-strand	195-200	6	93
α-helix	203-248	46
α-helix	255-258	4
α-helix	263-291	29
α-helix	294-298	5
β-strand	316-327	12	94
β-strand	330-341	12	94
β-strand	345-349	5	95
α-helix	356-364	9
β-strand	371-376	6	94
β-strand	382-385	4	95
α-helix	389-391	3
β-strand	397	1	96
α-helix	398-402	5
α-helix	407-419	13
α-helix	424-427	4
β-strand	430	1	96
α-helix	431-433	3
α-helix	436-448	13
β-strand	454-458	5	95
α-helix	466-478	13
β-strand	482-486	5	95
α-helix	490-496	7
β-strand	499-504	6	95
β-strand	507-511	5	95
α-helix	515-519	5
α-helix	527-547	21
α-helix	555-574	20

Chain b: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	90
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-35	5	90
β-strand	38-41	4	90
α-helix	43-62	20
β-strand	67-70	4	91
α-helix	77-87	11
β-strand	90-92	3	91
α-helix	96-97	2
α-helix	104-122	19
α-helix	125-128	4
α-helix	131-148	18
α-helix	149-151	3
β-strand	160-164	5	91
α-helix	170-178	9
β-strand	183-187	5	91
α-helix	193-195	3
β-strand	198-201	4	91
α-helix	207-225	19

Chain c: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	12	1	69
β-strand	16	1	69
β-strand	20	1	70
α-helix	28-45	18
β-strand	51-59	9	70
β-strand	62-69	8	70
α-helix	72-76	5
α-helix	78-80	3
α-helix	81-94	14
β-strand	97-104	8	70
α-helix	108-110	3
α-helix	112-124	13
α-helix	129-142	14
β-strand	147-154	8	71
α-helix	156-158	3
β-strand	163-170	8	71
β-strand	181-190	10	71
β-strand	193-202	10	71

38 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	2927	Bacillus subtilis subsp. subtilis str. 168
5S rRNA	B	RNA	119	Bacillus subtilis subsp. subtilis str. 168
50S ribosomal protein L2	C	protein	277	Bacillus subtilis subsp. subtilis str. 168	P42919 (AlphaFold model)
50S ribosomal protein L3	D	protein	209	Bacillus subtilis subsp. subtilis str. 168	P42920 (AlphaFold model)
50S ribosomal protein L4	E	protein	207	Bacillus subtilis subsp. subtilis str. 168	P42921 (AlphaFold model)
50S ribosomal protein L5	F	protein	179	Bacillus subtilis subsp. subtilis str. 168	P12877 (AlphaFold model)
50S ribosomal protein L6	G	protein	179	Bacillus subtilis subsp. subtilis str. 168	P46898
50S ribosomal protein L13	J	protein	145	Bacillus subtilis subsp. subtilis str. 168	P70974
50S ribosomal protein L14	K	protein	122	Bacillus subtilis subsp. subtilis str. 168	P12875
50S ribosomal protein L15	L	protein	146	Bacillus subtilis subsp. subtilis str. 168	P19946
50S ribosomal protein L16	M	protein	144	Bacillus subtilis subsp. subtilis str. 168	P14577
50S ribosomal protein L17	N	protein	120	Bacillus subtilis subsp. subtilis str. 168	P20277

39 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8BUU_1 23S rRNA (chains A)
GGUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGG
ACGAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUG
GGGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAG
GCAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCC
CUGAGUAGCGGCGAGCGAAACGGGAUUAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUG
UAGGACACUCUGUACGGAGUUACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCC
GCCAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCUCUCCUGAGUGGAUCCUGAGU
ACGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUAC
UCCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGG
GGAGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGA
UGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCCCGUGCAAGGUUAAGCAGAAG
AUGCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGACCC
GAAACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCG
AACCCACGCACGUUGAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGA
ACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGUCU
UGGAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAACU
CCGAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAA
AGGGAAACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUG
UGGAGUUGCUUAGACAACUAGGAUGUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGU
AAUAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGGCUAAACGUAUCACCG
AAGCUGCGGACUGUUCUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGA
CCGGAAGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGG
UGAGAAUCCCCUCCACCGAAUGCCUAAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUU
AGUCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAACAGGUUGAUAUUCCUG
UACCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAU
UGGAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGGCU
GAGCUGUGAUGGCGAGCGAAAUAUAGUAGCGAAGUUCCUGAUUCCACACUGCCAAGAAAA
GCCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAGAA
UCCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCG
GGAGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGC
GACUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACG
CCUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGAAG
CCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGU
AAGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGU
GAAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGA
GCUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCCUU
GGAAACCGGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGA
CCUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGG
GGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAA
UCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGG
GACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAU
AAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGU
UUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCAGUCCCAAGGGUUGGGC
UGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCC
CUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGA
UGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCG
GACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAU
UCCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGU
GGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACCA

Sequence of entity 2 (B), FASTA

>8BUU_2 5S rRNA (chains B)
UUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUC
UUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGCAAG

Sequence of entity 3 (C), FASTA

>8BUU_3 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 4 (D), FASTA

>8BUU_4 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK

Sequence of entity 5 (E), FASTA

>8BUU_5 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 6 (F), FASTA

>8BUU_6 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK

Sequence of entity 7 (G), FASTA

>8BUU_7 50S ribosomal protein L6 (chains G)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK

Sequence of entity 8 (J), FASTA

>8BUU_8 50S ribosomal protein L13 (chains J)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG

Sequence of entity 9 (K), FASTA

>8BUU_9 50S ribosomal protein L14 (chains K)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI

Sequence of entity 10 (L), FASTA

>8BUU_10 50S ribosomal protein L15 (chains L)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI

Sequence of entity 11 (M), FASTA

>8BUU_11 50S ribosomal protein L16 (chains M)
MLLPKRVKYRREHRGKMRGRAKGGTEVHFGEFGIQALEASWITNRQIEAARIAMTRYMKR
GGKVWIKIFPSKPYTAKPLEVRMGSGKGAPEGWVAVVKPGKVLFEISGVSEEVAREALRL
ASHKLPIKTKFVKREEIGGESNES

Sequence of entity 12 (N), FASTA

>8BUU_12 50S ribosomal protein L17 (chains N)
MSYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGKRGDLHARR
QAAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTRIMKLGPRRGDGAPMAIIELV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	85
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
ZN	Zinc ion	Zn	4

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

Primary citation

Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR. Obana, N., Takada, H., Crowe-McAuliffe, C. et al. Nucleic Acids Res (2023) 51:4536-4554. DOI 10.1093/nar/gkad193 · PubMed

Other PDB entries of the same protein (UniProt P42919 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8S1P 1.96 Å, YlmH bound to PtRNA-50S
8QCQ 2.3 Å, B. subtilis ApdA-stalled ribosomal complex
9FY1 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in…
9FY2 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-site
9FY3 2.8 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
7AS8 2.9 Å, Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with…
7AQC 2.99 Å, Structure of the bacterial RQC complex (Decoding State)
7SAE 3.0 Å, 44SR70P Class1 ribosomal particle
6TNN 3.07 Å, Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA
6TPQ 3.07 Å, RNase M5 bound to 50S ribosome with precursor 5S rRNA
6HA1 3.1 Å, Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader…
7AQD 3.1 Å, Structure of the bacterial RQC complex (Translocating State)

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