4W2F: Thermus thermophilus 70S ribosome

Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites. Determined by X-ray diffraction at 2.4 Å resolution. Released 15 Oct 2014.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Thermus thermophilus, synthetic construct, Escherichia coli
Chains: 112
Atoms: 298,643
Mol. weight: 4558.56 kDa
Ligands: MG, UAM, SF4, ZN
Released: 15 Oct 2014

Explore 4W2F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4W2F contains 507 α-helices and 639 β-strands across 98 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	26-31	6
β-strand	32-35	4	2
β-strand	40-42	3	2
α-helix	44-62	19
β-strand	69-71	3	3
α-helix	78-88	11
β-strand	92-93	2	3
α-helix	105-108	4
α-helix	109-111	3
α-helix	112-121	10
α-helix	132-149	18
β-strand	162-164	3	3
α-helix	171-178	8
β-strand	184-186	3	3
α-helix	194-196	3
β-strand	199-200	2	3
α-helix	208-227	20

Chain AC: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	12	1	14
β-strand	16	1	14
β-strand	20	1	15
α-helix	26-28	3
α-helix	30-46	17
β-strand	52-56	5	16
β-strand	57	1	15
β-strand	59	1	17
β-strand	63-64	2	17
β-strand	67-70	4	16
α-helix	73-77	5
α-helix	83-95	13
β-strand	98-99	2	17
β-strand	102-105	4	16
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-155	8	18
α-helix	157-159	3
β-strand	164-171	8	18
β-strand	181-191	11	18
β-strand	194-205	12	18

Chains AD and CD: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	25-27	3
α-helix	32-35	4
α-helix	47-52	6
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	26
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	27
β-strand	131-132	2	27
β-strand	139	1	26
β-strand	144-148	5	27
α-helix	150-152	3
α-helix	156-163	8
α-helix	168-171	4
β-strand	174-177	4	27
β-strand	182-185	4	27
α-helix	188-190	3
α-helix	200-208	9

Chain AE: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-19	13	32
β-strand	24-35	12	32
β-strand	41-48	8	32
α-helix	51-63	13
β-strand	66-67	2	32
β-strand	72	1	33
β-strand	75	1	33
β-strand	80-84	5	34
β-strand	87-93	7	34
β-strand	100-101	2	34
α-helix	104-113	10
β-strand	118-124	7	34
α-helix	128-139	12
α-helix	145-151	7

Chains AF and CF: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	39
α-helix	16-32	17
β-strand	36-52	17	39
β-strand	55-67	13	39
α-helix	69-71	3
α-helix	72-80	9
β-strand	85-92	8	39
β-strand	98-99	2	40

Chain AG: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	13-15	3
α-helix	21-30	10
α-helix	36-52	17
α-helix	58-68	11
β-strand	73-78	6	56
β-strand	85-90	6	56
α-helix	91-92	2
α-helix	93-108	16
α-helix	116-128	13
α-helix	133-147	15
α-helix	149-151	3

Chain AH: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	23-27	5	71
α-helix	30-41	12
β-strand	47-53	7	71
β-strand	56-62	7	71
β-strand	65	1	72
α-helix	67-70	4
α-helix	75-77	3
β-strand	78	1	72
β-strand	83-85	3	73
β-strand	94-95	2	73
α-helix	97-99	3
α-helix	100-102	3
α-helix	103-106	4
β-strand	109-114	6	73
β-strand	117-120	4	73
α-helix	121-127	7
β-strand	131-137	7	73

Chain AI: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	81
β-strand	13-21	9	81
β-strand	26-28	3	81
β-strand	31-32	2	81
α-helix	33-36	4
α-helix	41-45	5
α-helix	49-52	4
β-strand	59-66	8	81
α-helix	70-88	19
α-helix	90-92	3
α-helix	109-112	4
α-helix	122-125	4

79 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	1521	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

43 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4W2F_1 16S Ribosomal RNA (chains AA, CA)
UUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAA
GUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGG
GUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGAC
CCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUC
AGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUG
GCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAU
CUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGG
GUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAA
UAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCG
GAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGG
CUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAU
UCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCA
CCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCC
GGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCU
AACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGA
CGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA
CCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCC
CUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCC
GCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGAC
UGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCU
GGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUA
AUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGA
AUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACA
CCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGC
GCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUG
CGGCUGGAUCACCUCCUUUCU

Sequence of entity 2 (AB, CB), FASTA

>4W2F_2 30S Ribosomal Protein S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC, CC), FASTA

>4W2F_3 30S Ribosomal Protein S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD, CD), FASTA

>4W2F_4 30S Ribosomal Protein S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4W2F_5 30S Ribosomal Protein S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF, CF), FASTA

>4W2F_6 30S Ribosomal Protein S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4W2F_7 30S Ribosomal Protein S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4W2F_8 30S Ribosomal Protein S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4W2F_9 30S Ribosomal Protein S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4W2F_10 30S Ribosomal Protein S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK, CK), FASTA

>4W2F_11 30S Ribosomal Protein S11 (chains AK, CK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4W2F_12 30S Ribosomal Protein S12 (chains AL, CL)
MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG
YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK
KPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2307
UAM	Amicoumacin A	C20 H29 N3 O7	2
SF4	Iron/sulfur cluster	Fe4 S4	2
ZN	Zinc ion	Zn	12

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

Primary citation

Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome. Polikanov, Y.S., Osterman, I.A., Szal, T. et al. Mol Cell (2014) 56:531-540. DOI 10.1016/j.molcel.2014.09.020 · 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…
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…
9MTP 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…

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