4V9Q: Blasticidin S

Name: PDB 4V9Q: Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome. Determined by X-ray diffraction at 3.4 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Thermus thermophilus, Escherichia coli, Synthetic DNA
Chains: 108
Atoms: 293,113
Mol. weight: 4417.69 kDa
Ligands: ZN, MG, BLS
Released: 9 Jul 2014

Explore 4V9Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V9Q contains 426 α-helices and 659 β-strands across 96 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.

Chains A1 and C1: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	215
β-strand	47-49	3	215
β-strand	56-57	2	215

Chains A2 and C2: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	13-19	7
α-helix	20-23	4
α-helix	24-29	6
β-strand	31-32	2	1
β-strand	39-40	2	1
β-strand	45	1	123

Chains A3 and C3: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	3
α-helix	14	1
β-strand	15	1	4
β-strand	23-25	3	3
β-strand	38-39	2	5
β-strand	47-48	2	5
β-strand	49	1	4

Chains A4 and C4: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-23	6
α-helix	25-35	11

Chains A5 and C5: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	8-11	4
β-strand	15-16	2	23
β-strand	22-25	4	23
α-helix	26	1
α-helix	38-43	6
β-strand	47-49	3	23
α-helix	52-59	8

Chain AD: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	7
β-strand	17-19	3	7
β-strand	36	1	8
β-strand	54	1	9
β-strand	63	1	8
β-strand	65	1	10
α-helix	70-72	3
β-strand	73	1	11
β-strand	76-83	8	12
β-strand	92-97	6	12
β-strand	102-103	2	12
β-strand	104	1	10
β-strand	106	1	12
β-strand	108	1	13
β-strand	116-118	3	12
β-strand	119	1	11
β-strand	130	1	11
α-helix	133-135	3
α-helix	137	1
β-strand	141-146	6	11
β-strand	153-155	3	11
β-strand	163-169	7	11
β-strand	171-176	6	11
β-strand	182-186	5	11
β-strand	191-193	3	11
β-strand	196	1	13
α-helix	199-203	5
α-helix	209-214	6
β-strand	217	1	9
α-helix	218-220	3
α-helix	223-225	3
α-helix	240-242	3
β-strand	247	1	14
β-strand	253	1	14
α-helix	265-269	5
β-strand	270	1	11

Chains AE and CE: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	16
β-strand	14-15	2	17
β-strand	20-21	2	17
β-strand	24-27	4	16
β-strand	31-32	2	18
β-strand	33-37	5	19
β-strand	46-53	8	19
α-helix	58-60	3
α-helix	63-68	6
α-helix	73-74	2
β-strand	75-82	8	19
β-strand	90-91	2	18
α-helix	93-95	3
β-strand	98	1	20
β-strand	100	1	20
β-strand	101-107	7	16
β-strand	110-114	5	21
α-helix	116-119	4
β-strand	144	1	22
β-strand	147	1	22
α-helix	150-151	2
β-strand	158-161	4	21
β-strand	164-176	13	16
β-strand	181-184	4	16
β-strand	195-200	6	16

Chains AF and CF: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	27
β-strand	16-19	4	27
α-helix	30-43	14
α-helix	91-94	4
α-helix	103-119	17
β-strand	123-126	4	27
α-helix	136-144	9
β-strand	154-157	4	27
α-helix	161-168	8
β-strand	173-176	4	27
α-helix	178-180	3
α-helix	183-188	6
β-strand	191-195	5	27
α-helix	196-205	10

51 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 ribosomal RNA	AA, CA	RNA	2879	Thermus thermophilus
5S ribosomal RNA	AB, CB	RNA	119	Thermus thermophilus
50S ribosomal protein L2	AD, CD	protein	271	Thermus thermophilus	Q72I07 (AlphaFold model)
50S ribosomal protein L3	AE, CE	protein	204	Thermus thermophilus	Q72I04 (AlphaFold model)
50S ribosomal protein L4	AF, CF	protein	202	Thermus thermophilus	Q72I05 (AlphaFold model)
50S ribosomal protein L5	AG, CG	protein	181	Thermus thermophilus	Q72I16 (AlphaFold model)
50S ribosomal protein L6	AH, CH	protein	159	Thermus thermophilus	Q72I19
50S ribosomal protein L9	AI, CI	protein	145	Thermus thermophilus	Q72GV5
50S ribosomal protein L13	AJ, CJ	protein	137	Thermus thermophilus	Q72IN1
50S ribosomal protein L14	AK, CK	protein	122	Thermus thermophilus	Q72I14
50S ribosomal protein L15	AL, CL	protein	146	Thermus thermophilus	Q72I23
50S ribosomal protein L16	AM, CM	protein	134	Thermus thermophilus	Q72I11

41 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V9Q_1 23S ribosomal RNA (chains AA, CA)
AGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGCUACC
UGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGGGGAA
CCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUUGCGCGGGGGGAACCUGGGGAACUGA
AACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAGCGA
AAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGCAACC
GAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCCGUA
GGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCAUGG
GGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCACCAG
UACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAACCGU
GGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGAGCC
GGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCGAGU
CCGAACAGGGCGUCUAGUCCGCGGCCGUGGACCCGAAACCGGGCGAGCUAGCCCUGGCCA
GGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGAACCGGUGGGGGAUGCAAACCCCUCG
GAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAGCCCGGAGAUAGCUGGUUCUCCCCGA
AAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGGGCCUGUAGAGCACUGAUAGGGCUAG
GGGGCCCACCAGCCUACCAAACCCUGUCAAACUCCGAAGGGUCCCAGGUGGAGCCUGGGA
GUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCGCGGGAACAACCGAGACCGCCAGCUA
AGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGUGGCGCCGCGAAGACAGCCAGGAGGU
UGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGGCGCCG
CGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGAAGCUGCGGGUCUGGGGGAUGACCCC
AGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGGCGGCUGGAGGU
AAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAAAGAGGGUGAGAAUCCCUCUCGCCGU
AAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGUAGGGUUAGGCGGGACCUAAGGUGAA
GCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUAUUCCGGCCCUUCCCGCAGGUGCGAU
GGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAUGGACGAGCCCGGCCAGAAGCGCAGG
GUGGGAGGUAGGCAAAUCCGCCUCCCAAAAGCUCUGCGUGGUGGGGAAGCCCGUACGGGU
GACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCUCUAAGCACAACCUGCGGGAACCCG
UACCGCAAACCGACACAGGUGGGCGGGUGCAAGAGCACUCAGGCGCGCGGGAGAACCCUC
GCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUCGGGAGAAGGGGUGCUCCCUGGGGUGA
UGAGCUCCGGGGAGCCGCAGUGAACAGGCUCUGGCGACUGUUUACCAAAAACACAGCUCU
CUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGACGCUUGCCCGGUGCCGGAAGGUCAAGG
GGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCC
UAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAAGCGUAACGACCGG
AGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGAACUGGCCGUGAAGAUGCGGCCUACCC
GUGGCAGGACGAAAAGACCCCGUGGAGCUUUACUGCAGCCUGGUGUUGGCUCUUGGUCGC
GCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCCG
GUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAACCCUCGGAUGGGGGGACAGCGCUUGG
CGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUCCCC
UCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAGGGUAGAAGGGGGCCUGACUGCGAGGC
CUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAGUGAACCGGUGGUCCCGUGUGGAAGGG
CCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGCGUCC
ACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAG
GUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCG
UGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCAGGAGGCUUGAGGGGGGCUCUUCCUAG
UACGAGAGGACCGGAAGGGACGCACCUCUGGUUUCCCAGCUGUCCCUCCAGGGGCAUAAG
CUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCCGCCCC
AAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAGGACCCGGGAAGACUACCCGGUGGAUG
GGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCCGACCGGUCCCAAUCGUCCGAGGUCU

Sequence of entity 2 (AB, CB), FASTA

>4V9Q_2 5S ribosomal RNA (chains AB, CB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGG

Sequence of entity 3 (AD, CD), FASTA

>4V9Q_3 50S ribosomal protein L2 (chains AD, CD)
AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKRL
YRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAGP
DAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGE
LRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAP
RGRPPASPWGWQTKGLKTRKRRKPSSRFIIA

Sequence of entity 4 (AE, CE), FASTA

>4V9Q_4 50S ribosomal protein L3 (chains AE, CE)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKA

Sequence of entity 5 (AF, CF), FASTA

>4V9Q_5 50S ribosomal protein L4 (chains AF, CF)
MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIW
PQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLL
VEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYD
IVRTERLVMDLDAWEVFQNRIG

Sequence of entity 6 (AG, CG), FASTA

>4V9Q_6 50S ribosomal protein L5 (chains AG, CG)
PLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELA
LITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLN
PNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFR
K

Sequence of entity 7 (AH, CH), FASTA

>4V9Q_7 50S ribosomal protein L6 (chains AH, CH)
PKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRHKSLHGLTRTL
IANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEGITFEVPEPTRV
RVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVR

Sequence of entity 8 (AI, CI), FASTA

>4V9Q_8 50S ribosomal protein L9 (chains AI, CI)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVV

Sequence of entity 9 (AJ, CJ), FASTA

>4V9Q_9 50S ribosomal protein L13 (chains AJ, CJ)
KTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIR
VTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK
VYAGPDHPHQAQRPEKL

Sequence of entity 10 (AK, CK), FASTA

>4V9Q_10 50S ribosomal protein L14 (chains AK, CK)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL

Sequence of entity 11 (AL, CL), FASTA

>4V9Q_11 50S ribosomal protein L15 (chains AL, CL)
DLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLMRLPK
RGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEAKPLK
VVAHAFSKSALEKLKAAGGEPVLLEA

Sequence of entity 12 (AM, CM), FASTA

>4V9Q_12 50S ribosomal protein L16 (chains AM, CM)
RMKYRKQQRGRLKGATKGGDYVAFGDFGLVALEPAWITAQQIEAARVAMVRHFRRGGKIF
IRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRIAGHKL
PIKTKIVRRDAYDE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
MG	Magnesium ion	Mg	4363
BLS	Blasticidin S	C17 H26 N8 O5	2

Primary citation

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome. Svidritskiy, E., Ling, C., Ermolenko, D.N. et al. Proc Natl Acad Sci U S A (2013) 110:12283-12288. DOI 10.1073/pnas.1304922110 · PubMed

Other PDB entries of the same protein (UniProt Q72I07 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J4D 3.1 Å, E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated…
6N1D 3.2 Å, X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into…
4V63 3.21 Å, Structural basis for translation termination on the 70S ribosome.
5V8I 3.25 Å, Thermus thermophilus 70S ribosome lacking ribosomal protein uS17
4V84 3.4 Å, Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S…
4V9N 3.4 Å, Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
6B4V 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome
6BOH 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304)…
4V83 3.5 Å, Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to…
4V9K 3.5 Å, 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP,…
4V9L 3.5 Å, 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC…
6BOK 3.55 Å, E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome

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