4V5E: 30S ribosomal protein S2

Name: PDB 4V5E: Insights into translational termination from the structure of RF2 bound to the ribosome
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Insights into translational termination from the structure of RF2 bound to the ribosome. Determined by X-ray diffraction at 3.45 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.45 Å
Organisms: THERMUS THERMOPHILUS, Escherichia coli K-12, synthetic construct
Chains: 118
Atoms: 304,505
Mol. weight: 4641 kDa
Ligands: MG, ZN
Released: 9 Jul 2014

Explore 4V5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V5E contains 423 α-helices and 714 β-strands across 106 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.

Chains AB and CB: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6
β-strand	19	1	11
α-helix	26-28	3
β-strand	34	1	12
α-helix	36-38	3
β-strand	40	1	11
β-strand	41	1	12
α-helix	44-60	17
α-helix	62-64	3
β-strand	69-71	3	13
α-helix	75-77	3
α-helix	79-86	8
β-strand	92-93	2	13
α-helix	105-122	18
α-helix	125-127	3
α-helix	132-148	17
β-strand	162-164	3	13
α-helix	171-179	9
β-strand	184-186	3	13
β-strand	199-200	2	13
α-helix	208-223	16

Chain AC: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	21	1	18
α-helix	29-45	17
β-strand	56	1	19
β-strand	58	1	18
β-strand	63-64	2	20
β-strand	67	1	19
α-helix	73-77	5
α-helix	83-92	10
β-strand	98-99	2	20
α-helix	109-111	3
α-helix	113-125	13
α-helix	132-143	12
β-strand	148-150	3	21
β-strand	151-153	3	22
α-helix	157-159	3
β-strand	166	1	22
β-strand	169-171	3	21
β-strand	182-188	7	22
β-strand	197-203	7	22

Chains AD and CD: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	53-66	14
α-helix	72-83	12
α-helix	89-96	8
β-strand	100	1	31
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	32
β-strand	132	1	32
β-strand	139	1	31
β-strand	145	1	33
β-strand	146-148	3	32
α-helix	150-152	3
α-helix	156-165	10
β-strand	174-177	4	33
β-strand	182-185	4	33
α-helix	191-193	3
α-helix	200-205	6

Chains AE and CE: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	38
β-strand	17-20	4	39
β-strand	23-26	4	39
β-strand	28-35	8	38
β-strand	40-48	9	38
α-helix	51-63	13
β-strand	66-68	3	38
β-strand	80-84	5	40
β-strand	87-93	7	40
β-strand	100-101	2	40
α-helix	106-113	8
β-strand	118-124	7	40
α-helix	128-139	12
α-helix	142-144	3
α-helix	145-151	7

Chains AF and CF: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	48
α-helix	20-32	13
β-strand	41-52	12	48
β-strand	55-67	13	48
α-helix	72-79	8
β-strand	85-92	8	48
β-strand	98	1	49

Chains AG and CG: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-67	10
β-strand	73-76	4	62
β-strand	87-90	4	62
α-helix	93-109	17
α-helix	117-127	11
α-helix	133-147	15
α-helix	151-153	3

Chain AH: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	23-24	2	72
α-helix	30-40	11
β-strand	45-47	3	72
β-strand	50	1	73
β-strand	59	1	73
β-strand	61-63	3	72
β-strand	65	1	74
α-helix	75-77	3
β-strand	78	1	74
β-strand	83-85	3	75
β-strand	95	1	76
α-helix	103-105	3
β-strand	109	1	75
β-strand	111-115	5	77
β-strand	117-120	4	77
α-helix	121-127	7
β-strand	131	1	76
β-strand	132	1	77
β-strand	135-137	3	75

Chains AI and CI: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	82
β-strand	14-21	8	82
β-strand	26-28	3	82
β-strand	32	1	82
α-helix	33-36	4
α-helix	43-45	3
β-strand	59-66	8	82
α-helix	70-87	18
α-helix	123-125	3

58 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, CA	RNA	1522	THERMUS THERMOPHILUS
30S ribosomal protein S2	AB, CB	protein	256	THERMUS THERMOPHILUS	P80371 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	239	THERMUS THERMOPHILUS	P80372 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	209	THERMUS THERMOPHILUS	P80373 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	162	THERMUS THERMOPHILUS	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	THERMUS THERMOPHILUS	Q5SLP8
30S ribosomal protein S7	AG, CG	protein	156	THERMUS THERMOPHILUS	P17291
30S ribosomal protein S8	AH, CH	protein	138	THERMUS THERMOPHILUS	P0DOY9
30S ribosomal protein S9	AI, CI	protein	128	THERMUS THERMOPHILUS	P80374
30S ribosomal protein S10	AJ, CJ	protein	105	THERMUS THERMOPHILUS	Q5SHN7
30S ribosomal protein S11	AK, CK	protein	129	THERMUS THERMOPHILUS	P80376
30S ribosomal protein S12	AL, CL	protein	132	THERMUS THERMOPHILUS	Q5SHN3

47 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V5E_1 16S ribosomal RNA (chains AA, CA)
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, CB), FASTA

>4V5E_2 30S RIBOSOMAL PROTEIN S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC, CC), FASTA

>4V5E_3 30S RIBOSOMAL PROTEIN S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD, CD), FASTA

>4V5E_4 30S RIBOSOMAL PROTEIN S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4V5E_5 30S RIBOSOMAL PROTEIN S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF, CF), FASTA

>4V5E_6 30S RIBOSOMAL PROTEIN S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4V5E_7 30S RIBOSOMAL PROTEIN S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4V5E_8 30S RIBOSOMAL PROTEIN S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4V5E_9 30S RIBOSOMAL PROTEIN S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V5E_10 30S RIBOSOMAL PROTEIN S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK, CK), FASTA

>4V5E_11 30S RIBOSOMAL PROTEIN S11 (chains AK, CK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4V5E_12 30S RIBOSOMAL PROTEIN S12 (chains AL, CL)
MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG
YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK
KPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1092
ZN	Zinc ion	Zn	6

Primary citation

Insights Into Translational Termination from the Structure of Rf2 Bound to the Ribosome. Weixlbaumer, A., Jin, H., Neubauer, C. et al. Science (2008) 322:953-956. DOI 10.1126/science.1164840 · 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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