4V51: Thermus thermophilus 70S ribosome

Name: PDB 4V51: Structure of the Thermus thermophilus 70S ribosome complexed with mRNA, tRNA and paromomycin
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the Thermus thermophilus 70S ribosome complexed with mRNA, tRNA and paromomycin. Determined by X-ray diffraction at 2.8 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: THERMUS THERMOPHILUS, Escherichia coli K-12, synthetic construct
Chains: 112
Atoms: 291,075
Mol. weight: 4494.24 kDa
Ligands: ZN, PAR, MG
Released: 9 Jul 2014

Explore 4V51 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V51 contains 378 α-helices and 614 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.

Chain AB: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
β-strand	19	1	8
α-helix	26-30	5
β-strand	34-36	3	8
β-strand	39-41	3	8
α-helix	44-62	19
β-strand	69-71	3	9
α-helix	75-77	3
α-helix	78-86	9
β-strand	92-93	2	9
α-helix	102-104	3
α-helix	105-122	18
α-helix	125-128	4
α-helix	132-149	18
β-strand	162-164	3	9
α-helix	168-170	3
α-helix	171-179	9
β-strand	184-188	5	9
β-strand	199-202	4	9
α-helix	208-224	17

Chain AC: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	17-18	2
β-strand	21	1	17
α-helix	30-45	16
α-helix	48-50	3
β-strand	52	1	18
β-strand	58	1	17
β-strand	59	1	19
β-strand	63-64	2	19
β-strand	68-69	2	20
β-strand	70	1	18
α-helix	73-75	3
α-helix	84-94	11
β-strand	98-99	2	19
β-strand	103-104	2	20
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-142	13
β-strand	148-153	6	21
α-helix	157-159	3
β-strand	166	1	21
β-strand	169-171	3	21
β-strand	182-187	6	21
β-strand	198-203	6	21

Chains AD and CD: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	53-68	16
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	132	1	27
β-strand	139	1	26
α-helix	140-141	2
β-strand	145-148	4	27
α-helix	152-154	3
α-helix	156-165	10
β-strand	174-176	3	27
β-strand	182-185	4	27
α-helix	188-190	3
α-helix	191-193	3
α-helix	200-206	7

Chains AE and CE: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	9-20	12	41
β-strand	23-35	13	41
β-strand	40-48	9	41
α-helix	51-63	13
β-strand	66-68	3	41
β-strand	72	1	42
β-strand	75	1	42
β-strand	80-81	2	43
β-strand	84	1	43
β-strand	87-92	6	43
β-strand	100-101	2	43
α-helix	104-113	10
β-strand	117	1	42
β-strand	118-124	7	43
α-helix	128-139	12
α-helix	145-149	5

Chain AF: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	51
α-helix	16-32	17
β-strand	36-37	2	51
β-strand	44	1	51
β-strand	47	1	52
β-strand	57	1	52
β-strand	59-66	8	51
α-helix	72-80	9
β-strand	85-88	4	51
β-strand	92	1	51
β-strand	98	1	53

Chain AG: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	13-15	3
α-helix	21-30	10
α-helix	36-47	12
α-helix	58-67	10
β-strand	74-76	3	59
β-strand	87-89	3	59
α-helix	93-110	18
α-helix	116-129	14
α-helix	133-147	15
α-helix	150-152	3

Chain AH: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	23-27	5	68
α-helix	28	1
α-helix	30-41	12
β-strand	45-50	6	68
β-strand	58-63	6	68
β-strand	65	1	69
α-helix	75-77	3
β-strand	78	1	69
β-strand	83-85	3	70
β-strand	88	1	71
β-strand	91	1	71
β-strand	94-95	2	72
α-helix	103-106	4
β-strand	109	1	70
β-strand	112-114	3	73
β-strand	117-119	3	73
α-helix	123-127	5
β-strand	131-132	2	72
β-strand	135-137	3	70

Chains AI and CI: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	82
β-strand	14-18	5	82
β-strand	19-21	3	83
β-strand	27-28	2	84
β-strand	31-32	2	84
α-helix	33-36	4
α-helix	43-45	3
α-helix	50-52	3
β-strand	59-61	3	83
β-strand	62-63	2	84
β-strand	64-66	3	82
α-helix	70-87	18
α-helix	93-96	4
β-strand	118	1	85
β-strand	121	1	85

56 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	1522	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	P62669
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	135	THERMUS THERMOPHILUS	Q5SHN3

43 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V51_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
GCGGCUGGAUCACCUCCUUUCU

Sequence of entity 2 (AB, CB), FASTA

>4V51_2 30S RIBOSOMAL PROTEIN S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC, CC), FASTA

>4V51_3 30S RIBOSOMAL PROTEIN S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD, CD), FASTA

>4V51_4 30S RIBOSOMAL PROTEIN S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4V51_5 30S RIBOSOMAL PROTEIN S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF, CF), FASTA

>4V51_6 30S RIBOSOMAL PROTEIN S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4V51_7 30S RIBOSOMAL PROTEIN S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4V51_8 30S RIBOSOMAL PROTEIN S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4V51_9 30S RIBOSOMAL PROTEIN S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V51_10 30S RIBOSOMAL PROTEIN S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK, CK), FASTA

>4V51_11 30S RIBOSOMAL PROTEIN S11 (chains AK, CK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4V51_12 30S RIBOSOMAL PROTEIN S12 (chains AL, CL)
MVALPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL
TSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKY
GTKKPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
PAR	Paromomycin	C23 H45 N5 O14	2
MG	Magnesium ion	Mg	1379

Primary citation

Structure of the 70S ribosome complexed with mRNA and tRNA. Selmer, M., Dunham, C.M., Murphy, F.V. et al. Science (2006) 313:1935-1942. DOI 10.1126/science.1131127 · 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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