4V7L: Viomycin

The structures of viomycin bound to the 70S ribosome. Determined by X-ray diffraction at 3.0 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Thermus thermophilus, Escherichia coli, Streptomyces puniceus
Chains: 116
Atoms: 294,559
Mol. weight: 4569.8 kDa
Ligands: MG, ZN
Released: 9 Jul 2014

Explore 4V7L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V7L contains 376 α-helices and 625 β-strands across 100 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 AB: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	26-31	6
β-strand	34-36	3	5
β-strand	39-41	3	5
α-helix	42-43	2
α-helix	44-62	19
β-strand	69-71	3	6
α-helix	78-83	6
α-helix	105-109	5
α-helix	113-116	4
α-helix	132-149	18
β-strand	162-164	3	6
α-helix	168-170	3
α-helix	171-179	9
β-strand	184-186	3	6
β-strand	199-200	2	6
α-helix	209-223	15

Chain AC: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	13
β-strand	28	1	13
α-helix	30-45	16
α-helix	48-50	3
β-strand	56	1	14
β-strand	64	1	15
β-strand	67	1	14
α-helix	73-75	3
α-helix	87-90	4
α-helix	91-93	3
β-strand	99	1	15
α-helix	113-124	12
α-helix	130-143	14
β-strand	148-153	6	16
α-helix	157-159	3
β-strand	169-171	3	16
β-strand	182-183	2	17
β-strand	187	1	16
β-strand	198-201	4	16
β-strand	202-203	2	17

Chain AD: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	50-52	3
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	23
α-helix	101-107	7
α-helix	114-121	8
β-strand	126	1	24
β-strand	127	1	25
β-strand	132	1	25
β-strand	139	1	23
β-strand	144	1	26
β-strand	148	1	24
α-helix	156-163	8
β-strand	166	1	27
β-strand	168	1	27
β-strand	174-177	4	26
α-helix	178-180	3
β-strand	182-185	4	26
α-helix	191-193	3
α-helix	200-206	7

Chain AE: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	39
β-strand	14-15	2	39
β-strand	18-20	3	40
β-strand	23-25	3	40
β-strand	28-35	8	39
β-strand	40	1	41
β-strand	41-48	8	39
α-helix	51-64	14
β-strand	68	1	41
β-strand	80-84	5	42
β-strand	87-93	7	42
α-helix	94-95	2
β-strand	100-101	2	42
α-helix	107-113	7
β-strand	118-121	4	42
β-strand	124	1	42
α-helix	128-139	12
α-helix	145-149	5

Chain AF: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	52
β-strand	8-10	3	53
α-helix	16-32	17
β-strand	36-37	2	52
β-strand	44-52	9	53
β-strand	55-60	6	53
β-strand	63-67	5	52
α-helix	72-80	9
β-strand	85-88	4	53
β-strand	91	1	52
β-strand	98-99	2	54

Chain AG: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-28	8
α-helix	36-52	17
α-helix	58-67	10
β-strand	73-77	5	59
β-strand	86-90	5	59
α-helix	95-109	15
α-helix	116-127	12
α-helix	133-147	15
α-helix	149-152	4

Chain AH: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	23-24	2	64
β-strand	27	1	65
α-helix	30-42	13
β-strand	47	1	64
β-strand	50-53	4	65
β-strand	56-59	4	65
β-strand	61-62	2	64
α-helix	63-64	2
β-strand	65	1	66
β-strand	78	1	66
β-strand	83-85	3	67
β-strand	88	1	68
β-strand	91	1	68
β-strand	94-95	2	69
α-helix	104-106	3
β-strand	109-112	4	67
β-strand	119	1	67
α-helix	121-123	3
α-helix	124-128	5
β-strand	131-132	2	69
β-strand	133-137	5	67

Chain AI: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	76
β-strand	13-19	7	76
β-strand	21	1	77
β-strand	27-28	2	76
β-strand	32	1	76
α-helix	33-36	4
α-helix	43-45	3
α-helix	48-50	3
β-strand	59	1	77
β-strand	62-66	5	76
α-helix	70-87	18
α-helix	93-95	3
α-helix	96-100	5
α-helix	109-111	3
β-strand	118	1	78
β-strand	121	1	78
α-helix	122-125	4

92 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
16S ribosomal RNA	AA, CA	RNA	1509	Thermus thermophilus
30S ribosomal protein S2	AB, CB	protein	256	Thermus thermophilus	P80371 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	239	Thermus thermophilus	P80372 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	209	Thermus thermophilus	P80373 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	162	Thermus thermophilus	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	Thermus thermophilus	Q5SLP8
30S ribosomal protein S7	AG, CG	protein	156	Thermus thermophilus	P17291
30S ribosomal protein S8	AH, CH	protein	138	Thermus thermophilus	P0DOY9
30S ribosomal protein S9	AI, CI	protein	128	Thermus thermophilus	P80374
30S ribosomal protein S10	AJ, CJ	protein	105	Thermus thermophilus	Q5SHN7
30S ribosomal protein S11	AK, CK	protein	129	Thermus thermophilus	P80376
30S ribosomal protein S12	AL, CL	protein	132	Thermus thermophilus	Q5SHN3

46 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V7L_1 16S ribosomal RNA (chains AA, CA)
UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCA
AGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUG
GGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGA
CCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAU
CAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAU
GGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAA
UCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGG
GGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUA
AUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCC
GGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACG
GCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAA
UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCC
ACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACC
CGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGC
UAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUG
ACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUU
ACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGC
CCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCC
CGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGA
CUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCC
UGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCU
AAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGG
AAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACAC
ACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGG
CGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGU
GCGGCUGGA

Sequence of entity 2 (AB, CB), FASTA

>4V7L_2 30S ribosomal protein S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC, CC), FASTA

>4V7L_3 30S ribosomal protein S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD, CD), FASTA

>4V7L_4 30S ribosomal protein S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4V7L_5 30S ribosomal protein S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF, CF), FASTA

>4V7L_6 30S ribosomal protein S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4V7L_7 30S ribosomal protein S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4V7L_8 30S ribosomal protein S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4V7L_9 30S ribosomal protein S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V7L_10 30S ribosomal protein S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK, CK), FASTA

>4V7L_11 30S ribosomal protein S11 (chains AK, CK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4V7L_12 30S ribosomal protein S12 (chains AL, CL)
MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG
YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK
KPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	965
ZN	Zinc ion	Zn	8

Primary citation

The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Stanley, R.E., Blaha, G., Grodzicki, R.L. et al. Nat Struct Mol Biol (2010) 17:289-293. DOI 10.1038/nsmb.1755 · PubMed

Other PDB entries of the same protein (UniProt P80371 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
4Y4O 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and…
8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
8VTX 2.4 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…

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