4V5M: 30S ribosomal protein S2

Name: PDB 4V5M: tRNA tranlocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE)
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

tRNA tranlocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE). Determined by electron microscopy at 7.8 Å resolution. Released 9 Jul 2014.

Method: Electron microscopy
Resolution: 7.8 Å
Organisms: THERMUS THERMOPHILUS, ESCHERICHIA COLI
Chains: 57
Atoms: 152,777
Mol. weight: 2311.3 kDa
Ligands: FUA, GDP
Released: 9 Jul 2014

Explore 4V5M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V5M contains 222 α-helices and 400 β-strands across 52 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	6
α-helix	26-31	6
β-strand	32-34	3	7
α-helix	36-38	3
β-strand	40	1	6
β-strand	41-42	2	7
α-helix	44-62	19
β-strand	69-71	3	8
α-helix	75-77	3
α-helix	78-86	9
β-strand	92-93	2	8
α-helix	105-122	18
α-helix	125-127	3
α-helix	132-149	18
β-strand	162-164	3	8
α-helix	168-170	3
α-helix	171-179	9
β-strand	184-186	3	8
α-helix	194-196	3
β-strand	199-200	2	8
α-helix	208-223	16

Chain AC: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	11
α-helix	29-45	17
β-strand	54-56	3	12
β-strand	57-58	2	11
β-strand	64	1	13
β-strand	67-69	3	12
α-helix	73-77	5
α-helix	84-92	9
β-strand	99	1	13
β-strand	102-104	3	12
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-153	6	14
α-helix	157-159	3
β-strand	166	1	14
β-strand	169-171	3	14
β-strand	182-191	10	14
β-strand	194-203	10	14

Chain AD: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
α-helix	48-52	5
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	20
α-helix	101-108	8
α-helix	114-122	9
β-strand	126-128	3	21
β-strand	132	1	21
β-strand	139	1	20
α-helix	140-141	2
β-strand	145	1	22
β-strand	146-148	3	21
α-helix	156-164	9
β-strand	174-177	4	22
β-strand	182-185	4	22
α-helix	200-206	7

Chain AE: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-20	12	30
β-strand	23-35	13	30
β-strand	40-48	9	30
α-helix	51-64	14
β-strand	66-68	3	30
β-strand	80-84	5	31
β-strand	87-93	7	31
β-strand	100-101	2	31
α-helix	104-113	10
β-strand	118-124	7	31
α-helix	128-139	12
α-helix	145-148	4

Chain AF: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	41
β-strand	8-10	3	42
α-helix	16-32	17
β-strand	37	1	41
β-strand	44-47	4	42
β-strand	57-60	4	42
β-strand	64-67	4	41
α-helix	72-79	8
β-strand	85-88	4	42
β-strand	92	1	41
β-strand	98-99	2	43

Chain AG: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-69	12
β-strand	73-81	9	44
β-strand	83-90	8	44
α-helix	93-108	16
α-helix	116-129	14
α-helix	133-147	15
α-helix	150-152	3

Chain AH: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	23-27	5	47
α-helix	32-41	10
β-strand	47	1	47
β-strand	50-53	4	47
β-strand	56-62	7	47
α-helix	63	1
β-strand	65	1	48
α-helix	66-68	3
α-helix	76-77	2
β-strand	78	1	48
β-strand	83-85	3	49
β-strand	94-95	2	50
α-helix	104-106	3
β-strand	109	1	49
β-strand	111-115	5	50
β-strand	117-120	4	50
α-helix	121-127	7
β-strand	131-133	3	50
β-strand	135-137	3	49

Chain AI: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	53
β-strand	14-19	6	53
β-strand	21	1	54
β-strand	27-28	2	53
β-strand	32	1	53
α-helix	33-36	4
α-helix	43-47	5
α-helix	48-51	4
β-strand	59	1	54
β-strand	62-66	5	53
α-helix	70-84	15
α-helix	109-113	5
α-helix	122-125	4

44 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	AA	RNA	1522	THERMUS THERMOPHILUS
30S ribosomal protein S2	AB	protein	256	THERMUS THERMOPHILUS	P80371 (AlphaFold model)
30S ribosomal protein S3	AC	protein	239	THERMUS THERMOPHILUS	P80372 (AlphaFold model)
30S ribosomal protein S4	AD	protein	209	THERMUS THERMOPHILUS	P80373 (AlphaFold model)
30S ribosomal protein S5	AE	protein	162	THERMUS THERMOPHILUS	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	AF	protein	101	THERMUS THERMOPHILUS	Q5SLP8
30S ribosomal protein S7	AG	protein	156	THERMUS THERMOPHILUS	P17291
30S ribosomal protein S8	AH	protein	138	THERMUS THERMOPHILUS	P0DOY9
30S ribosomal protein S9	AI	protein	128	THERMUS THERMOPHILUS	P80374
30S ribosomal protein S10	AJ	protein	105	THERMUS THERMOPHILUS	Q5SHN7
30S ribosomal protein S11	AK	protein	129	THERMUS THERMOPHILUS	P80376
30S ribosomal protein S12	AL	protein	132	THERMUS THERMOPHILUS	Q5SHN3

45 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>4V5M_1 16S RRNA (chains AA)
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), FASTA

>4V5M_2 30S RIBOSOMAL PROTEIN S2 (chains AB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC), FASTA

>4V5M_3 30S RIBOSOMAL PROTEIN S3 (chains AC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD), FASTA

>4V5M_4 30S RIBOSOMAL PROTEIN S4 (chains AD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE), FASTA

>4V5M_5 30S RIBOSOMAL PROTEIN S5 (chains AE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF), FASTA

>4V5M_6 30S RIBOSOMAL PROTEIN S6 (chains AF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG), FASTA

>4V5M_7 30S RIBOSOMAL PROTEIN S7 (chains AG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH), FASTA

>4V5M_8 30S RIBOSOMAL PROTEIN S8 (chains AH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI), FASTA

>4V5M_9 30S RIBOSOMAL PROTEIN S9 (chains AI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ), FASTA

>4V5M_10 30S RIBOSOMAL PROTEIN S10 (chains AJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK), FASTA

>4V5M_11 30S RIBOSOMAL PROTEIN S11 (chains AK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL), FASTA

>4V5M_12 30S RIBOSOMAL PROTEIN S12 (chains AL)
MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG
YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK
KPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
FUA	Fusidic acid	C31 H48 O6	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Head Swivel on the Ribosome Facilitates Translocation by Means of Intra-Subunit tRNA Hybrid Sites. Ratje, A.H., Loerke, J., Mikolajka, A. et al. Nature (2010) 468:713. DOI 10.1038/NATURE09547 · 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

About this viewer

MolViewer shows 4V5M directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.