2VQE: 30S ribosomal protein S2

Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding. Determined by X-ray diffraction at 2.5 Å resolution. Released 29 Apr 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: THERMUS THERMOPHILUS
Chains: 23
Atoms: 52,245
Mol. weight: 799.28 kDa
Ligands: MG, PAR, ZN
Released: 29 Apr 2008

Explore 2VQE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VQE contains 105 α-helices and 116 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	1
α-helix	26-28	3
β-strand	32-36	5	1
β-strand	39-42	4	1
α-helix	44-62	19
β-strand	68-71	4	2
β-strand	92-93	2	2
α-helix	105-121	17
α-helix	132-135	4
α-helix	138-148	11
α-helix	152-154	3
β-strand	161-164	4	2
α-helix	171-179	9
β-strand	185-186	2	2
α-helix	194-196	3
β-strand	199-200	2	2
α-helix	208-223	16
α-helix	230-231	2
α-helix	233	1

Chain C: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	3
α-helix	29-44	16
β-strand	52-55	4	4
β-strand	57	1	3
β-strand	59	1	5
β-strand	64	1	5
β-strand	67-70	4	4
α-helix	73-75	3
α-helix	83-94	12
β-strand	102-105	4	4
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-153	6	6
β-strand	166	1	6
β-strand	169-171	3	6
α-helix	178-180	3
β-strand	182-187	6	6
β-strand	190	1	7
β-strand	195	1	7
β-strand	198-203	6	6

Chain D: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	33-35	3
α-helix	53-68	16
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	8
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	9
β-strand	131-132	2	9
β-strand	139	1	8
β-strand	145-148	4	9
α-helix	150-152	3
α-helix	156-164	9
β-strand	176-177	2	9
β-strand	182-184	3	9
α-helix	188-190	3
α-helix	191-193	3
α-helix	200-206	7

Chain E: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-20	14	10
β-strand	23-35	13	10
β-strand	40-48	9	10
α-helix	51-62	12
β-strand	66-68	3	10
β-strand	80-84	5	11
β-strand	87-93	7	11
β-strand	100-101	2	11
α-helix	104-111	8
β-strand	118-124	7	11
α-helix	128-141	14
α-helix	145-151	7

Chain F: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	12
α-helix	16-30	15
α-helix	31-33	3
β-strand	39-40	2	12
β-strand	44-52	9	12
β-strand	55-67	13	12
α-helix	69-71	3
α-helix	72-81	10
β-strand	85-92	8	12
β-strand	98-99	2	13

Chain G: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	13-15	3
α-helix	21-30	10
α-helix	36-49	14
α-helix	58-69	12
β-strand	73-76	4	14
β-strand	79	1	15
β-strand	84	1	15
β-strand	87-90	4	14
α-helix	93-108	16
α-helix	116-128	13
α-helix	133-144	12
α-helix	149-154	6

Chain H: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	27	1	16
α-helix	30-41	12
β-strand	47-53	7	16
β-strand	56-62	7	16
β-strand	65	1	17
α-helix	75-77	3
β-strand	78	1	17
β-strand	83-85	3	18
β-strand	88	1	19
β-strand	91	1	19
β-strand	94-95	2	18
α-helix	97-99	3
α-helix	103-106	4
β-strand	109-114	6	18
β-strand	117-120	4	18
α-helix	121-126	6
β-strand	131-137	7	18

Chain I: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	20
β-strand	9-10	2	20
β-strand	13-21	9	20
β-strand	26-28	3	20
β-strand	32	1	20
α-helix	33-36	4
α-helix	43-47	5
α-helix	48-53	6
β-strand	59-66	8	20
α-helix	70-88	19
α-helix	90-92	3
α-helix	93-96	4
β-strand	105	1	20
α-helix	109-111	3
β-strand	118	1	21
β-strand	121	1	21
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 rRNA	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	209	THERMUS THERMOPHILUS	P80373 (AlphaFold model)
30S ribosomal protein S5	E	protein	162	THERMUS THERMOPHILUS	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	F	protein	101	THERMUS THERMOPHILUS	Q5SLP8
30S ribosomal protein S7	G	protein	156	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	105	THERMUS THERMOPHILUS	Q5SHN7
30S ribosomal protein S11	K	protein	129	THERMUS THERMOPHILUS	P80376
30S ribosomal protein S12	L	protein	135	THERMUS THERMOPHILUS	Q5SHN3

11 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>2VQE_1 16S RRNA (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

>2VQE_2 30S RIBOSOMAL PROTEIN S2 (chains B)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (C), FASTA

>2VQE_3 30S RIBOSOMAL PROTEIN S3 (chains C)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (D), FASTA

>2VQE_4 30S RIBOSOMAL PROTEIN S4 (chains D)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (E), FASTA

>2VQE_5 30S RIBOSOMAL PROTEIN S5 (chains E)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (F), FASTA

>2VQE_6 30S RIBOSOMAL PROTEIN S6 (chains F)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (G), FASTA

>2VQE_7 30S RIBOSOMAL PROTEIN S7 (chains G)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (H), FASTA

>2VQE_8 30S RIBOSOMAL PROTEIN S8 (chains H)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (I), FASTA

>2VQE_9 30S RIBOSOMAL PROTEIN S9 (chains I)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (J), FASTA

>2VQE_10 30S RIBOSOMAL PROTEIN S10 (chains J)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (K), FASTA

>2VQE_11 30S RIBOSOMAL PROTEIN S11 (chains K)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (L), FASTA

>2VQE_12 30S RIBOSOMAL PROTEIN S12 (chains L)
MVALPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL
TSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKY
GTKKPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	206
PAR	Paromomycin	C23 H45 N5 O14	1
ZN	Zinc ion	Zn	2

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

Primary citation

Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding. Kurata, S., Weixlbaumer, A., Ohtsuki, T. et al. J Biol Chem (2008) 283:18801. DOI 10.1074/JBC.M800233200 · 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…

Browse structure collections

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