4V67: 30S ribosomal protein S2

Crystal structure of a translation termination complex formed with release factor RF2. Determined by X-ray diffraction at 3.0 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Thermus thermophilus, Escherichia coli
Chains: 112
Atoms: 301,148
Mol. weight: 4621.79 kDa
Ligands: ZN, MG
Released: 9 Jul 2014

Explore 4V67 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V67 contains 492 α-helices and 707 β-strands across 100 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: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6
α-helix	28-31	4
β-strand	32-36	5	34
β-strand	39-42	4	34
α-helix	44-63	20
α-helix	66-67	2
β-strand	68-71	4	35
α-helix	75-77	3
α-helix	78-86	9
β-strand	92-93	2	35
α-helix	105-121	17
α-helix	132-149	18
β-strand	161-164	4	35
α-helix	171-179	9
β-strand	184-188	5	35
α-helix	194-196	3
β-strand	199-202	4	35
α-helix	208-226	19
α-helix	232-233	2
α-helix	236-239	4

Chain AC: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	17-18	2
β-strand	20	1	43
α-helix	29-45	17
α-helix	48-50	3
β-strand	52-55	4	44
β-strand	57	1	43
β-strand	58-59	2	45
β-strand	63	1	46
β-strand	64-65	2	45
β-strand	68-70	3	44
α-helix	74-77	4
α-helix	83-92	10
β-strand	98	1	46
β-strand	103-104	2	44
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-155	8	47
α-helix	157-159	3
β-strand	164-166	3	47
β-strand	169-170	2	47
β-strand	182-187	6	47
β-strand	196-203	8	47

Chain AD: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	24-27	4
α-helix	48-52	5
α-helix	53-68	16
α-helix	72-84	13
α-helix	89-99	11
β-strand	100	1	63
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	64
β-strand	132	1	64
β-strand	139	1	63
β-strand	145-148	4	64
α-helix	150-153	4
α-helix	156-163	8
β-strand	174-177	4	64
β-strand	182-185	4	64
α-helix	188-190	3
α-helix	191-193	3
α-helix	200-206	7

Chain AE: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	75
β-strand	15	1	76
β-strand	18-20	3	77
β-strand	23-25	3	77
β-strand	28	1	76
β-strand	29-35	7	75
β-strand	40-47	8	75
α-helix	51-64	14
β-strand	67-68	2	75
β-strand	72	1	78
β-strand	75	1	78
β-strand	80-84	5	79
β-strand	87-93	7	79
β-strand	99-101	3	79
α-helix	104-112	9
β-strand	117-124	8	79
α-helix	128-139	12
α-helix	145-151	7

Chains AF and CF: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	87
α-helix	16-32	17
β-strand	36-37	2	87
β-strand	44	1	87
β-strand	47-52	6	88
β-strand	55-57	3	88
β-strand	59-62	4	87
β-strand	65-67	3	87
α-helix	69-71	3
α-helix	72-80	9
β-strand	85-92	8	87
α-helix	95-97	3
β-strand	98-99	2	89

Chains AG and CG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-68	11
β-strand	73-80	8	102
β-strand	83-90	8	102
α-helix	93-110	18
α-helix	116-129	14
α-helix	133-147	15
α-helix	148-154	7

Chain AH: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	23-24	2	117
β-strand	27	1	117
α-helix	30-41	12
β-strand	45-52	8	117
β-strand	57-63	7	117
β-strand	65	1	118
α-helix	67-70	4
β-strand	78	1	118
β-strand	83-85	3	119
β-strand	88	1	120
β-strand	91	1	120
β-strand	94-95	2	121
α-helix	97-99	3
α-helix	103-106	4
β-strand	109	1	119
β-strand	112	1	122
β-strand	119	1	122
α-helix	121-127	7
β-strand	131-132	2	121
β-strand	133	1	122
β-strand	135-137	3	119

Chains AI and CI: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	131
β-strand	13-21	9	131
β-strand	26-28	3	131
α-helix	33-36	4
α-helix	43-47	5
α-helix	48-51	4
β-strand	59-66	8	131
α-helix	70-87	18
α-helix	93-95	3
α-helix	122-124	3

54 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, CA	RNA	1525	Thermus thermophilus
P and E-site trna(fmet)	AY, AZ, CY, CZ	RNA	77	Escherichia coli
mRNA	AV, CV	RNA	27
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

43 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V67_1 16S RRNA (chains AA, CA)
AUUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGC
AAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGU
GGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGG
ACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCA
UCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGA
UGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGA
AUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCG
GGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGAGGAGGGGACUGACGGUACCGGGGU
AAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACC
CGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCAC
GGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGA
AUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGC
CACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUAC
CCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAG
CUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUU
GACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCU
UACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAG
CCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUC
CCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGG
ACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGC
CUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGC
UAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCG
GAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACA
CACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAG
GCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGG
UGCGGCUGGAUCACCUCCUUUCUAA

Sequence of entity 2 (AY, AZ, CY, CZ), FASTA

>4V67_2 P AND E-SITE TRNA(FMET) (chains AY, AZ, CY, CZ)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA

Sequence of entity 3 (AV, CV), FASTA

>4V67_3 MRNA (chains AV, CV)
GGCAAGGAGGUAAAAAUGUAAAAAAAA

Sequence of entity 4 (AB, CB), FASTA

>4V67_4 30S ribosomal protein S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 5 (AC, CC), FASTA

>4V67_5 30S ribosomal protein S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 6 (AD, CD), FASTA

>4V67_6 30S ribosomal protein S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 7 (AE, CE), FASTA

>4V67_7 30S ribosomal protein S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 8 (AF, CF), FASTA

>4V67_8 30S ribosomal protein S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 9 (AG, CG), FASTA

>4V67_9 30S ribosomal protein S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 10 (AH, CH), FASTA

>4V67_10 30S ribosomal protein S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 11 (AI, CI), FASTA

>4V67_11 30S ribosomal protein S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 12 (AJ, CJ), FASTA

>4V67_12 30S ribosomal protein S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
MG	Magnesium ion	Mg	2388

Primary citation

Crystal structure of a translation termination complex formed with release factor RF2. Korostelev, A., Asahara, H., Lancaster, L. et al. Proc Natl Acad Sci U S A (2008) 105:19684-19689. DOI 10.1073/pnas.0810953105 · 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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