4V90: Thermus thermophilus Ribosome

Name: PDB 4V90: Thermus thermophilus Ribosome
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Thermus thermophilus Ribosome. Determined by X-ray diffraction at 2.95 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: THERMUS THERMOPHILUS HB8, synthetic construct
Chains: 58
Atoms: 153,829
Mol. weight: 2320.93 kDa
Ligands: GCP, ZN, MG
Released: 9 Jul 2014

Explore 4V90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V90 contains 254 α-helices and 378 β-strands across 53 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-13	5
β-strand	32-34	3	1
β-strand	41-42	2	1
α-helix	47-63	17
β-strand	69-71	3	2
α-helix	78-86	9
β-strand	92-93	2	2
α-helix	105-121	17
α-helix	126-128	3
α-helix	132-147	16
α-helix	152-154	3
β-strand	162-164	3	2
α-helix	171-179	9
β-strand	184	1	2
α-helix	194-196	3
α-helix	208-224	17

Chain AC: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-50	3
β-strand	52-56	5	8
β-strand	64	1	9
β-strand	67-70	4	8
α-helix	73-76	4
α-helix	83-86	4
α-helix	87-93	7
β-strand	99	1	9
β-strand	102-104	3	8
α-helix	109-111	3
α-helix	113-116	4
α-helix	119-122	4
α-helix	132-143	12
β-strand	148-155	8	10
α-helix	157-159	3
β-strand	164-167	4	10
β-strand	170-171	2	10
β-strand	182-186	5	10
β-strand	189-191	3	11
β-strand	194-196	3	11
β-strand	197-203	7	10

Chain AD: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	25-27	3
β-strand	32	1	14
β-strand	35	1	14
α-helix	47-52	6
α-helix	53-68	16
α-helix	72-84	13
α-helix	89-99	11
β-strand	100	1	15
α-helix	101-108	8
α-helix	114-122	9
β-strand	127-128	2	16
β-strand	131-132	2	16
α-helix	138	1
β-strand	139	1	15
α-helix	140	1
β-strand	145	1	17
β-strand	146-147	2	16
α-helix	150-153	4
α-helix	156-163	8
β-strand	174-177	4	17
α-helix	178-180	3
β-strand	182-185	4	17
α-helix	200-206	7

Chain AE: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-19	11	22
β-strand	24-35	12	22
β-strand	40	1	23
β-strand	41-48	8	22
α-helix	51-63	13
β-strand	68	1	23
β-strand	72	1	24
β-strand	75	1	24
β-strand	80-84	5	25
β-strand	87-93	7	25
β-strand	100-101	2	25
α-helix	104-113	10
β-strand	118-124	7	25
α-helix	128-140	13
α-helix	145-151	7

Chain AF: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	32
α-helix	18-32	15
β-strand	36-37	2	32
β-strand	44-52	9	32
β-strand	55-61	7	32
β-strand	64-67	4	32
α-helix	69-80	12
β-strand	85-92	8	32
β-strand	98-99	2	33

Chain AG: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	9-13	5
α-helix	24-30	7
α-helix	38-45	8
α-helix	58-68	11
β-strand	73	1	38
β-strand	78	1	39
β-strand	85	1	39
β-strand	90	1	38
α-helix	93-108	16
α-helix	116-128	13
α-helix	133-147	15
α-helix	149-152	4

Chain AH: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	23-27	5	42
α-helix	30-41	12
β-strand	45-53	9	42
β-strand	56-63	8	42
β-strand	65	1	43
α-helix	76-77	2
β-strand	78	1	43
β-strand	83-85	3	44
β-strand	88	1	45
β-strand	91	1	45
β-strand	94-95	2	44
α-helix	103-106	4
β-strand	109-114	6	44
β-strand	117-120	4	44
α-helix	121-127	7
β-strand	131-137	7	44

Chain AI: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	47
β-strand	13-19	7	47
β-strand	21	1	48
β-strand	28	1	47
α-helix	43-45	3
α-helix	48-51	4
α-helix	56-58	3
β-strand	59	1	48
β-strand	62-63	2	47
β-strand	66	1	47
α-helix	70-87	18
α-helix	90-92	3
α-helix	93-96	4
α-helix	100-102	3
α-helix	110-113	4
β-strand	118	1	49
β-strand	121	1	49
α-helix	122-125	4

45 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	RNA	1519	THERMUS THERMOPHILUS HB8
30S ribosomal protein S2	AB	protein	256	THERMUS THERMOPHILUS HB8	P80371 (AlphaFold model)
30S ribosomal protein S3	AC	protein	239	THERMUS THERMOPHILUS HB8	P80372 (AlphaFold model)
30S ribosomal protein S4	AD	protein	209	THERMUS THERMOPHILUS HB8	P80373 (AlphaFold model)
30S ribosomal protein S5	AE	protein	162	THERMUS THERMOPHILUS HB8	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	AF	protein	101	THERMUS THERMOPHILUS HB8	Q5SLP8
30S ribosomal protein S7	AG	protein	156	THERMUS THERMOPHILUS HB8	P17291
30S ribosomal protein S8	AH	protein	138	THERMUS THERMOPHILUS HB8	P0DOY9
30S ribosomal protein S9	AI	protein	128	THERMUS THERMOPHILUS HB8	P80374
30S ribosomal protein S10	AJ	protein	105	THERMUS THERMOPHILUS HB8	Q5SHN7
30S ribosomal protein S11	AK	protein	129	THERMUS THERMOPHILUS HB8	P80376
30S ribosomal protein S12	AL	protein	132	THERMUS THERMOPHILUS HB8	Q5SHN3

46 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>4V90_1 16S RIBOSOMAL RNA (chains AA)
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
CGGCUGGAUCACCUCCUUU

Sequence of entity 2 (AB), FASTA

>4V90_2 30S RIBOSOMAL PROTEIN S2 (chains AB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC), FASTA

>4V90_3 30S RIBOSOMAL PROTEIN S3 (chains AC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD), FASTA

>4V90_4 30S RIBOSOMAL PROTEIN S4 (chains AD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE), FASTA

>4V90_5 30S RIBOSOMAL PROTEIN S5 (chains AE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF), FASTA

>4V90_6 30S RIBOSOMAL PROTEIN S6 (chains AF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG), FASTA

>4V90_7 30S RIBOSOMAL PROTEIN S7 (chains AG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH), FASTA

>4V90_8 30S RIBOSOMAL PROTEIN S8 (chains AH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI), FASTA

>4V90_9 30S RIBOSOMAL PROTEIN S9 (chains AI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ), FASTA

>4V90_10 30S RIBOSOMAL PROTEIN S10 (chains AJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK), FASTA

>4V90_11 30S RIBOSOMAL PROTEIN S11 (chains AK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL), FASTA

>4V90_12 30S RIBOSOMAL PROTEIN S12 (chains AL)
MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG
YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK
KPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
ZN	Zinc ion	Zn	3
MG	Magnesium ion	Mg	523

Primary citation

Structure of EF-G-ribosome complex in a pretranslocation state. Chen, Y., Feng, S., Kumar, V. et al. Nat Struct Mol Biol (2013) 20:1077-1084. DOI 10.1038/nsmb.2645 · 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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