4V8U: 30S ribosomal protein S2

Name: PDB 4V8U: Crystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex. Determined by X-ray diffraction at 3.7 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.7 Å
Organism: THERMUS THERMOPHILUS HB8
Chains: 114
Atoms: 307,606
Mol. weight: 4655.34 kDa
Ligands: ZN, FUA, GDP, MG
Released: 9 Jul 2014

Explore 4V8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V8U contains 458 α-helices and 789 β-strands across 102 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: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	26-31	6
β-strand	32-34	3	10
β-strand	41-42	2	10
α-helix	44-62	19
β-strand	68-71	4	11
α-helix	75-77	3
α-helix	78-86	9
β-strand	92-93	2	11
α-helix	105-113	9
α-helix	115-122	8
α-helix	125-127	3
α-helix	132-149	18
β-strand	161-164	4	11
α-helix	171-179	9
β-strand	184-186	3	11
β-strand	199-200	2	11
α-helix	208-224	17

Chains AC and CC: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	16
α-helix	29-45	17
α-helix	48-50	3
β-strand	52	1	17
β-strand	56	1	18
β-strand	57-58	2	16
β-strand	67-69	3	18
β-strand	70	1	17
α-helix	73-77	5
α-helix	83-91	9
α-helix	92-94	3
β-strand	102-104	3	18
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-153	6	19
α-helix	157-159	3
β-strand	166	1	19
β-strand	169-171	3	19
β-strand	182-191	10	19
β-strand	194-203	10	19

Chains AD and CD: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
α-helix	48-52	5
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-99	11
β-strand	100	1	25
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	26
β-strand	139	1	25
β-strand	145	1	27
β-strand	146-148	3	26
α-helix	149	1
α-helix	150-153	4
α-helix	156-163	8
β-strand	175	1	27
β-strand	184	1	27
α-helix	200-206	7

Chains AE and CE: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-19	11	54
β-strand	24-35	12	54
β-strand	40-48	9	54
α-helix	51-64	14
β-strand	66-68	3	54
β-strand	80-84	5	55
β-strand	87-93	7	55
β-strand	100-101	2	55
α-helix	104-113	10
β-strand	118-124	7	55
α-helix	128-139	12
α-helix	145-149	5

Chains AF and CF: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	66
β-strand	7-10	4	67
α-helix	16-32	17
β-strand	37	1	66
β-strand	44-47	4	67
β-strand	57-60	4	67
β-strand	63-67	5	66
α-helix	69-71	3
α-helix	72-79	8
β-strand	85-89	5	67
β-strand	92	1	66
β-strand	98-99	2	68

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	36-52	17
α-helix	58-65	8
α-helix	67-69	3
β-strand	73-76	4	78
β-strand	87-90	4	78
α-helix	93-108	16
α-helix	116-129	14
α-helix	133-147	15
α-helix	149-151	3

Chain AH: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	23-24	2	83
β-strand	27	1	83
α-helix	30-41	12
β-strand	45-53	9	83
β-strand	56-63	8	83
β-strand	65	1	84
α-helix	76-77	2
β-strand	78	1	84
β-strand	83-85	3	85
β-strand	88	1	86
β-strand	91	1	86
β-strand	94-95	2	87
α-helix	104-106	3
β-strand	109	1	85
β-strand	112-115	4	87
β-strand	117-119	3	87
α-helix	121-125	5
β-strand	131-133	3	87
β-strand	135-137	3	85

Chains AI and CI: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	99
β-strand	14-19	6	99
β-strand	21	1	100
β-strand	27-28	2	99
β-strand	32	1	99
α-helix	33-36	4
α-helix	43-45	3
α-helix	48-51	4
β-strand	59	1	100
β-strand	62-66	5	99
α-helix	70-84	15
α-helix	112-113	2
α-helix	122-125	4

60 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 HB8
30S ribosomal protein S2	AB, CB	protein	256	THERMUS THERMOPHILUS HB8	P80371 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	239	THERMUS THERMOPHILUS HB8	P80372 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	209	THERMUS THERMOPHILUS HB8	P80373 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	162	THERMUS THERMOPHILUS HB8	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	THERMUS THERMOPHILUS HB8	Q5SLP8
30S ribosomal protein S7	AG, CG	protein	156	THERMUS THERMOPHILUS HB8	P17291
30S ribosomal protein S8	AH, CH	protein	138	THERMUS THERMOPHILUS HB8	P0DOY9
30S ribosomal protein S9	AI, CI	protein	128	THERMUS THERMOPHILUS HB8	P80374
30S ribosomal protein S10	AJ, CJ	protein	105	THERMUS THERMOPHILUS HB8	Q5SHN7
30S ribosomal protein S11	AK, CK	protein	129	THERMUS THERMOPHILUS HB8	P80376
30S ribosomal protein S12	AL, CL	protein	132	THERMUS THERMOPHILUS HB8	Q5SHN3

45 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V8U_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

>4V8U_2 30S RIBOSOMAL PROTEIN S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC, CC), FASTA

>4V8U_3 30S RIBOSOMAL PROTEIN S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD, CD), FASTA

>4V8U_4 30S RIBOSOMAL PROTEIN S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4V8U_5 30S RIBOSOMAL PROTEIN S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF, CF), FASTA

>4V8U_6 30S RIBOSOMAL PROTEIN S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4V8U_7 30S RIBOSOMAL PROTEIN S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4V8U_8 30S RIBOSOMAL PROTEIN S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4V8U_9 30S RIBOSOMAL PROTEIN S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V8U_10 30S RIBOSOMAL PROTEIN S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK, CK), FASTA

>4V8U_11 30S RIBOSOMAL PROTEIN S11 (chains AK, CK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4V8U_12 30S RIBOSOMAL PROTEIN S12 (chains AL, CL)
MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG
YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK
KPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
FUA	Fusidic acid	C31 H48 O6	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	2

Primary citation

Crystal structure of 70S ribosome with both cognate tRNAs in the E and P sites representing an authentic elongation complex. Feng, S., Chen, Y., Gao, Y.G. PLoS One (2013) 8:e58829-e58829. DOI 10.1371/journal.pone.0058829 · 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 4V8U 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.