1J5E: Thermus thermophilus 30S Ribosomal Subunit

Structure of the Thermus thermophilus 30S Ribosomal Subunit. Determined by X-ray diffraction at 3.05 Å resolution. Released 12 Apr 2002.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Thermus thermophilus
Chains: 21
Atoms: 51,933
Mol. weight: 782.62 kDa
Ligands: ZN
Released: 12 Apr 2002

Explore 1J5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1J5E contains 104 α-helices and 109 β-strands across 20 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 B: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	26-31	6
β-strand	32-36	5	1
β-strand	39-42	4	1
α-helix	44-62	19
β-strand	69-71	3	2
α-helix	75-86	12
β-strand	92-93	2	2
α-helix	105-121	17
α-helix	126-128	3
α-helix	134-148	15
β-strand	162-164	3	2
α-helix	171-180	10
β-strand	184-188	5	2
α-helix	194-196	3
β-strand	199-202	4	2
α-helix	208-224	17
α-helix	236-239	4

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	29-46	18
β-strand	52-56	5	3
β-strand	67-70	4	3
α-helix	73-77	5
α-helix	83-92	10
β-strand	102-105	4	3
α-helix	109-111	3
α-helix	113-126	14
α-helix	130-142	13
β-strand	148-153	6	4
α-helix	157-159	3
β-strand	166	1	4
β-strand	169-170	2	4
β-strand	182-187	6	4
β-strand	198-203	6	4

Chain D: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	39	1
α-helix	47-49	3
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	5
α-helix	101-107	7
α-helix	114-122	9
β-strand	126	1	6
β-strand	127	1	7
β-strand	132	1	7
β-strand	139	1	5
β-strand	145	1	8
α-helix	147	1
β-strand	148	1	6
α-helix	149	1
α-helix	150-153	4
α-helix	156-164	9
β-strand	176-177	2	9
β-strand	182-183	2	9
β-strand	184	1	8
α-helix	188-190	3
α-helix	191-193	3
α-helix	200-206	7

Chain E: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	10
β-strand	19-20	2	11
β-strand	23-24	2	11
β-strand	28-35	8	10
β-strand	40-48	9	10
α-helix	51-63	13
β-strand	66-68	3	10
β-strand	72	1	12
β-strand	75	1	12
β-strand	80-84	5	13
β-strand	87-93	7	13
β-strand	100-101	2	13
α-helix	104-112	9
β-strand	118-124	7	13
α-helix	128-141	14
α-helix	145-151	7

Chain F: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	14
β-strand	4-10	7	15
α-helix	16-33	18
β-strand	39-52	14	15
β-strand	55-64	10	15
β-strand	66-67	2	14
α-helix	69-81	13
β-strand	85-92	8	15
β-strand	98-99	2	16

Chain G: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	21-30	10
α-helix	36-52	17
α-helix	58-69	12
β-strand	73-76	4	17
β-strand	79	1	18
β-strand	84	1	18
β-strand	87-90	4	17
α-helix	93-108	16
α-helix	116-129	14
α-helix	133-144	12
α-helix	151-154	4

Chain H: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	25-27	3	19
α-helix	30-41	12
β-strand	47-53	7	19
β-strand	56-62	7	19
β-strand	65	1	20
α-helix	75-77	3
β-strand	78	1	20
β-strand	83-85	3	21
β-strand	94-95	2	21
α-helix	103-106	4
β-strand	109-114	6	21
β-strand	117-120	4	21
α-helix	121-126	6
β-strand	131-137	7	21

Chain I: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	22
β-strand	9	1	22
β-strand	14-19	6	22
β-strand	26-28	3	22
β-strand	32	1	22
α-helix	33-36	4
α-helix	43-45	3
α-helix	48-52	5
β-strand	61-66	6	22
α-helix	70-88	19
α-helix	90-92	3
α-helix	93-96	4
α-helix	109-111	3
α-helix	122-124	3

12 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	A	RNA	1522	Thermus thermophilus
30S ribosomal protein S2	B	protein	256	Thermus thermophilus	P80371 (AlphaFold model)
30S ribosomal protein S3	C	protein	239	Thermus thermophilus	P80372 (AlphaFold model)
30S ribosomal protein S4	D	protein	208	Thermus thermophilus	P80373 (AlphaFold model)
30S ribosomal protein S5	E	protein	161	Thermus thermophilus	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	F	protein	101	Thermus thermophilus	Q5SLP8
30S ribosomal protein S7	G	protein	155	Thermus thermophilus	P17291
30S ribosomal protein S8	H	protein	138	Thermus thermophilus	P0DOY9
30S ribosomal protein S9	I	protein	128	Thermus thermophilus	P80374
30S ribosomal protein S10	J	protein	104	Thermus thermophilus	Q5SHN7
30S ribosomal protein S11	K	protein	129	Thermus thermophilus	P80376
30S ribosomal protein S12	L	protein	135	Thermus thermophilus	Q5SHN3

9 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>1J5E_1 16S ribosomal RNA (chains A)
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 (B), FASTA

>1J5E_2 30S RIBOSOMAL PROTEIN S2 (chains B)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (C), FASTA

>1J5E_3 30S RIBOSOMAL PROTEIN S3 (chains C)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (D), FASTA

>1J5E_4 30S RIBOSOMAL PROTEIN S4 (chains D)
GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREK
QKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLV
RHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGM
KGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (E), FASTA

>1J5E_5 30S RIBOSOMAL PROTEIN S5 (chains E)
PETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYY
ARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTK
ELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (F), FASTA

>1J5E_6 30S RIBOSOMAL PROTEIN S6 (chains F)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (G), FASTA

>1J5E_7 30S RIBOSOMAL PROTEIN S7 (chains G)
ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKV
FKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIA
HELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (H), FASTA

>1J5E_8 30S RIBOSOMAL PROTEIN S8 (chains H)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (I), FASTA

>1J5E_9 30S RIBOSOMAL PROTEIN S9 (chains I)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (J), FASTA

>1J5E_10 30S RIBOSOMAL PROTEIN S10 (chains J)
PKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSRE
HFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (K), FASTA

>1J5E_11 30S RIBOSOMAL PROTEIN S11 (chains K)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (L), FASTA

>1J5E_12 30S RIBOSOMAL PROTEIN S12 (chains L)
MVALPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL
TSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKY
GTKKPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Structure of the 30S ribosomal subunit. Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M. et al. Nature (2000) 407:327-339. DOI 10.1038/35030006 · 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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1J5E is part of these collections:

The ribosome and protein synthesis

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