4V9J: 30S ribosomal protein S2

70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state. Determined by X-ray diffraction at 3.86 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.86 Å
Organisms: Thermus thermophilus, Escherichia coli, Streptomyces
Chains: 122
Atoms: 308,202
Mol. weight: 4566.59 kDa
Ligands: GNP, MG
Released: 9 Jul 2014

Explore 4V9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V9J contains 422 α-helices and 705 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	28-31	4
β-strand	33	1	1
β-strand	41	1	1
α-helix	44-64	21
β-strand	68	1	2
β-strand	71	1	3
α-helix	75-88	14
β-strand	93	1	3
α-helix	105-120	16
α-helix	125-127	3
α-helix	132-148	17
α-helix	151-154	4
β-strand	161	1	2
α-helix	170-179	10
β-strand	187-188	2	4
β-strand	201-202	2	4
α-helix	208-225	18
α-helix	236-240	5

Chain AC: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	18
α-helix	26-28	3
α-helix	29-45	17
β-strand	52	1	19
β-strand	57-59	3	18
β-strand	64-66	3	18
β-strand	70	1	19
α-helix	74-77	4
α-helix	82-94	13
α-helix	113-125	13
α-helix	130-145	16
β-strand	148-155	8	20
β-strand	164	1	20
β-strand	169-171	3	20
β-strand	182-187	6	20
β-strand	190-191	2	21
β-strand	194-195	2	21
β-strand	196-203	8	20

Chain AD: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-97	9
β-strand	100	1	28
α-helix	101-108	8
α-helix	114-121	8
β-strand	126-128	3	29
β-strand	131-133	3	29
β-strand	139	1	28
β-strand	144-145	2	30
β-strand	146-148	3	29
α-helix	156-165	10
β-strand	174-177	4	30
β-strand	182-185	4	30
α-helix	200-207	8

Chain AE: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	38
β-strand	14-18	5	38
β-strand	25-34	10	38
β-strand	40-48	9	38
α-helix	51-64	14
β-strand	66-68	3	38
β-strand	72	1	39
β-strand	75	1	39
β-strand	80-83	4	40
β-strand	88-92	5	40
β-strand	100-101	2	40
α-helix	104-112	9
β-strand	118-123	6	40
α-helix	128-139	12
α-helix	145-151	7

Chain AF: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	49
α-helix	16-32	17
β-strand	36-37	2	49
β-strand	44-47	4	49
β-strand	57-67	11	49
α-helix	69-81	13
β-strand	85-92	8	49
β-strand	98	1	50

Chain AG: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-28	8
α-helix	36-53	18
α-helix	58-68	11
β-strand	73	1	55
β-strand	90	1	55
α-helix	93-109	17
α-helix	116-129	14
α-helix	133-147	15
α-helix	150-152	3

Chain AH: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	23-24	2	72
β-strand	27	1	72
α-helix	31-41	11
β-strand	45-53	9	72
β-strand	56-63	8	72
α-helix	67-69	3
β-strand	83	1	73
β-strand	94	1	73
α-helix	104-106	3
β-strand	109-114	6	73
β-strand	117-118	2	73
α-helix	121-127	7
β-strand	131-137	7	73

Chain AI: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	79
β-strand	14-20	7	79
β-strand	27-28	2	79
β-strand	31-32	2	79
α-helix	33-36	4
α-helix	42-47	6
α-helix	48-50	3
β-strand	60-66	7	79
α-helix	70-87	18
α-helix	90-92	3
α-helix	93-99	7
α-helix	122-125	4

93 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	P62662 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	207	Thermus thermophilus	P62663 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	208	Thermus thermophilus	P62664 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	151	Thermus thermophilus	P62665 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	Thermus thermophilus	P62666
30S ribosomal protein S7	AG, CG	protein	155	Thermus thermophilus	P62667
30S ribosomal protein S8	AH, CH	protein	138	Thermus thermophilus	P62668
30S ribosomal protein S9	AI, CI	protein	127	Thermus thermophilus	P62669
30S ribosomal protein S10	AJ, CJ	protein	99	Thermus thermophilus	P62653
30S ribosomal protein S11	AK, CK	protein	119	Thermus thermophilus	P62654
30S ribosomal protein S12	AL, CL	protein	125	Thermus thermophilus	P61941
30S ribosomal protein S13	AM, CM	protein	125	Thermus thermophilus	P62655

48 more molecules are not listed.

Sequence of entity 1 (AB, CB), FASTA

>4V9J_1 30S ribosomal protein S2 (chains AB, CB)
VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGG
TILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPE
IEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIA
LADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQE

Sequence of entity 2 (AC, CC), FASTA

>4V9J_2 30S ribosomal protein S3 (chains AC, CC)
GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAA
DNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVA
EQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRAN
IDYGFALARTTYGVLGVKAYIFLGEVI

Sequence of entity 3 (AD, CD), FASTA

>4V9J_3 30S ribosomal protein S4 (chains AD, CD)
GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREK
QKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLV
RHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGM
KGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 4 (AE, CE), FASTA

>4V9J_4 30S ribosomal protein S5 (chains AE, CE)
DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARR
NMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELG
SRNPINIAYATMEALRQLRTKADVERLRKGE

Sequence of entity 5 (AF, CF), FASTA

>4V9J_5 30S ribosomal protein S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 6 (AG, CG), FASTA

>4V9J_6 30S ribosomal protein S7 (chains AG, CG)
ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKV
FKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIA
HELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 7 (AH, CH), FASTA

>4V9J_7 30S ribosomal protein S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 8 (AI, CI), FASTA

>4V9J_8 30S ribosomal protein S9 (chains AI, CI)
EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDA
YITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARR
APQYSKR

Sequence of entity 9 (AJ, CJ), FASTA

>4V9J_9 30S ribosomal protein S10 (chains AJ, CJ)
KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREH
FELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTV

Sequence of entity 10 (AK, CK), FASTA

>4V9J_10 30S ribosomal protein S11 (chains AK, CK)
KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAK
KAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS

Sequence of entity 11 (AL, CL), FASTA

>4V9J_11 30S ribosomal protein S12 (chains AL, CL)
PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGY
EVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKK
PKEAA

Sequence of entity 12 (AM, CM), FASTA

>4V9J_12 30S ribosomal protein S13 (chains AM, CM)
ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE
NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKK
KAPRK

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Zhou, J., Lancaster, L., Donohue, J.P. et al. Science (2013) 340:1236086-1236086. DOI 10.1126/science.1236086 · 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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