4W29: 30S ribosomal protein S2

70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic acid, mRNA, and tRNAs trapped in the AP/AP pe/E chimeric hybrid state. Determined by X-ray diffraction at 3.8 Å resolution. Released 1 Oct 2014.

Method: X-ray diffraction
Resolution: 3.8 Å
Organisms: Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039), Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Thermus thermophilus HB27
Chains: 122
Atoms: 312,066
Mol. weight: 4630.82 kDa
Ligands: MG, NMY, FUA, GDP
Released: 1 Oct 2014

Explore 4W29 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4W29 contains 411 α-helices and 719 β-strands across 104 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	26-30	5
β-strand	32-33	2	1
α-helix	36-38	3
α-helix	40	1
β-strand	41-42	2	1
α-helix	44-64	21
β-strand	70-71	2	2
α-helix	75-88	14
β-strand	92-93	2	2
α-helix	105-122	18
α-helix	132-148	17
α-helix	169-179	11
α-helix	183-184	2
β-strand	185-188	4	3
β-strand	199-202	4	3
α-helix	208-225	18
α-helix	236-239	4

Chain AC: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	20-22	3	16
α-helix	26-46	21
β-strand	57-59	3	16
β-strand	64-65	2	16
β-strand	70	1	17
α-helix	74-77	4
α-helix	83-94	12
β-strand	105	1	17
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-152	5	18
β-strand	155	1	19
β-strand	164	1	19
β-strand	167-171	5	18
β-strand	182-188	7	18
β-strand	191	1	20
β-strand	194	1	20
β-strand	197-203	7	18

Chain AD: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	23-26	4
α-helix	53-68	16
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	35
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	36
β-strand	131-132	2	36
β-strand	139	1	35
β-strand	145	1	37
β-strand	146-148	3	36
α-helix	157-163	7
β-strand	175-177	3	37
β-strand	182-184	3	37
α-helix	200-207	8

Chain AE: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	60
β-strand	20	1	61
β-strand	23	1	61
β-strand	28-35	8	60
β-strand	41-48	8	60
α-helix	51-62	12
β-strand	66-67	2	60
β-strand	81-84	4	62
β-strand	87-93	7	62
β-strand	100-101	2	62
α-helix	104-113	10
β-strand	118-124	7	62
α-helix	128-140	13
α-helix	145-153	9

Chain AF: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	70
α-helix	16-33	18
β-strand	36-46	11	70
β-strand	58-67	10	70
α-helix	71-81	11
β-strand	85-92	8	70
β-strand	98-99	2	71

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-68	11
β-strand	73-81	9	73
β-strand	83-90	8	73
α-helix	91-92	2
α-helix	93-110	18
α-helix	116-129	14
α-helix	133-147	15
α-helix	150-153	4

Chain AH: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	23-27	5	77
α-helix	30-41	12
β-strand	51-53	3	77
β-strand	56-62	7	77
β-strand	65	1	78
α-helix	76-77	2
β-strand	78	1	78
β-strand	83-85	3	79
β-strand	94-95	2	79
β-strand	109-114	6	79
β-strand	117-120	4	79
α-helix	121-127	7
β-strand	131-137	7	79

Chain AI: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	81
β-strand	13-19	7	81
β-strand	26-28	3	81
β-strand	31-32	2	81
α-helix	33-36	4
α-helix	42-46	5
α-helix	48-52	5
β-strand	61-67	7	81
α-helix	70-88	19
α-helix	122-125	4

95 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
30S ribosomal protein S2	AB, CB	protein	235	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62662 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	207	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62663 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	208	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62664 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	151	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62665 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62666
30S ribosomal protein S7	AG, CG	protein	155	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62667
30S ribosomal protein S8	AH, CH	protein	138	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62668
30S ribosomal protein S9	AI, CI	protein	127	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	P80374
30S ribosomal protein S10	AJ, CJ	protein	99	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62653
30S ribosomal protein S11	AK, CK	protein	119	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62654
30S ribosomal protein S12	AL, CL	protein	125	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P61941
30S ribosomal protein S13	AM, CM	protein	125	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62655

48 more molecules are not listed.

Sequence of entity 1 (AB, CB), FASTA

>4W29_1 30S ribosomal protein S2 (chains AB, CB)
VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGG
TILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPE
IEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIA
LADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQE

Sequence of entity 2 (AC, CC), FASTA

>4W29_2 30S ribosomal protein S3 (chains AC, CC)
GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAA
DNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVA
EQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRAN
IDYGFALARTTYGVLGVKAYIFLGEVI

Sequence of entity 3 (AD, CD), FASTA

>4W29_3 30S ribosomal protein S4 (chains AD, CD)
GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREK
QKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLV
RHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGM
KGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 4 (AE, CE), FASTA

>4W29_4 30S ribosomal protein S5 (chains AE, CE)
DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARR
NMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELG
SRNPINIAYATMEALRQLRTKADVERLRKGE

Sequence of entity 5 (AF, CF), FASTA

>4W29_5 30S ribosomal protein S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 6 (AG, CG), FASTA

>4W29_6 30S ribosomal protein S7 (chains AG, CG)
ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKV
FKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIA
HELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 7 (AH, CH), FASTA

>4W29_7 30S ribosomal protein S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 8 (AI, CI), FASTA

>4W29_8 30S ribosomal protein S9 (chains AI, CI)
EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDA
YITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARR
APQYSKR

Sequence of entity 9 (AJ, CJ), FASTA

>4W29_9 30S ribosomal protein S10 (chains AJ, CJ)
KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREH
FELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTV

Sequence of entity 10 (AK, CK), FASTA

>4W29_10 30S ribosomal protein S11 (chains AK, CK)
KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAK
KAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS

Sequence of entity 11 (AL, CL), FASTA

>4W29_11 30S ribosomal protein S12 (chains AL, CL)
PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGY
EVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKK
PKEAA

Sequence of entity 12 (AM, CM), FASTA

>4W29_12 30S ribosomal protein S13 (chains AM, CM)
ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE
NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKK
KAPRK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
NMY	Neomycin	C23 H46 N6 O13	6
FUA	Fusidic acid	C31 H48 O6	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation. Zhou, J., Lancaster, L., Donohue, J.P. et al. Science (2014) 345:1188-1191. DOI 10.1126/science.1255030 · PubMed

Other PDB entries of the same protein (UniProt P62662 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J4D 3.1 Å, E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated…
6N1D 3.2 Å, X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into…
4V63 3.21 Å, Structural basis for translation termination on the 70S ribosome.
5V8I 3.25 Å, Thermus thermophilus 70S ribosome lacking ribosomal protein uS17
4V84 3.4 Å, Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S…
4V9N 3.4 Å, Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
4V9Q 3.4 Å, Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.
6B4V 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome
6BOH 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304)…
4V83 3.5 Å, Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to…
4V9K 3.5 Å, 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP,…
4V9L 3.5 Å, 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC…

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