4V9D: 30S ribosomal protein S2

Name: PDB 4V9D: Structures of the bacterial ribosome in classical and hybrid states of tRNA binding
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Determined by X-ray diffraction at 3.0 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Escherichia coli
Chains: 109
Atoms: 292,354
Mol. weight: 4322.35 kDa
Ligands: MG, ZN
Released: 9 Jul 2014

Explore 4V9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V9D contains 443 α-helices and 662 β-strands across 99 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: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	24-29	6
β-strand	30	1	9
β-strand	40	1	9
α-helix	46-48	3
α-helix	52-61	10
β-strand	68-69	2	10
α-helix	82-85	4
β-strand	90-91	2	10
α-helix	107-117	11
α-helix	137-144	8
β-strand	161-164	4	10
α-helix	166-168	3
α-helix	169-178	10
β-strand	183-185	3	10
β-strand	197-198	2	10
α-helix	206-220	15

Chain AC: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	25-45	21
β-strand	51-55	5	19
β-strand	63	1	20
β-strand	66-69	4	19
α-helix	72-76	5
α-helix	81-94	14
β-strand	98	1	20
β-strand	101	1	19
β-strand	104	1	19
α-helix	108-110	3
α-helix	112-125	14
α-helix	129-141	13
β-strand	147-151	5	21
β-strand	168-169	2	21
β-strand	181-190	10	21
β-strand	193-202	10	21

Chain AD: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	49-64	16
α-helix	68-80	13
α-helix	85-94	10
β-strand	96	1	38
α-helix	99-102	4
α-helix	110-118	9
β-strand	123	1	39
β-strand	128	1	39
β-strand	135	1	38
β-strand	140	1	40
β-strand	143	1	39
α-helix	152-161	10
β-strand	172	1	41
β-strand	178	1	39
β-strand	179	1	41
β-strand	181	1	40
α-helix	198-204	7

Chain AE: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	12-19	8	53
β-strand	32-39	8	53
β-strand	45-48	4	53
β-strand	51-52	2	53
α-helix	55-67	13
β-strand	84-88	5	54
β-strand	91-96	6	54
β-strand	105	1	54
α-helix	111-116	6
β-strand	123-128	6	54
α-helix	132-145	14
α-helix	151-155	5

Chain AF: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	64
β-strand	9-10	2	65
α-helix	12-14	3
α-helix	17-30	14
β-strand	35	1	64
β-strand	40-45	6	65
α-helix	46-47	2
β-strand	57-61	5	65
β-strand	64-66	3	64
α-helix	72-80	9
β-strand	84-86	3	65

Chain AG: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	20-29	10
α-helix	35-50	16
α-helix	58-68	11
β-strand	72-74	3	79
β-strand	87-89	3	79
α-helix	92-108	17
α-helix	115-127	13
α-helix	133-146	14
α-helix	147-149	3

Chain AH: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	23-25	3	90
α-helix	30-41	12
β-strand	45-47	3	90
β-strand	50	1	91
β-strand	58	1	91
β-strand	59-62	4	90
β-strand	64	1	92
β-strand	69	1	92
β-strand	75-76	2	93
β-strand	85-86	2	94
β-strand	100	1	95
β-strand	103-106	4	96
β-strand	108-110	3	96
α-helix	112-118	7
β-strand	122-123	2	94
β-strand	124	1	96
β-strand	126-127	2	93
β-strand	128	1	95

Chain AI: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	108
β-strand	15-22	8	108
β-strand	27-29	3	108
β-strand	32	1	108
α-helix	49-51	3
β-strand	60-67	8	108
α-helix	71-83	13
α-helix	109-113	5
β-strand	119	1	109
β-strand	122	1	109
α-helix	123-125	3

89 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, BA	RNA	1539	Escherichia coli
30S ribosomal protein S2	AB, BB	protein	218	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC, BC	protein	206	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD, BD	protein	205	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE, BE	protein	150	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF, BF	protein	100	Escherichia coli	P02358
30S ribosomal protein S7	AG, BG	protein	151	Escherichia coli	P02359
30S ribosomal protein S8	AH, BH	protein	129	Escherichia coli	P0A7W7
30S ribosomal protein S9	AI, BI	protein	127	Escherichia coli	P0A7X3
30S ribosomal protein S10	AJ, BJ	protein	98	Escherichia coli	P0A7R5
30S ribosomal protein S11	AK, BK	protein	117	Escherichia coli	P0A7R9
30S ribosomal protein S12	AL, BL	protein	123	Escherichia coli	P0A7S3

45 more molecules are not listed.

Sequence of entity 1 (AA, BA), FASTA

>4V9D_1 16S rRNA (chains AA, BA)
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAG
UCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAU
GUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUA
ACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGG
GAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAG
GAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGG
GAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUU
CGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUG
ACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGG
GUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAG
AUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCG
UAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG
GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAA
ACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCC
UUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAA
GGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUU
CGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGA
AUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAA
AUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCC
GGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA
UCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGA
CCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACU
CGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUU
CCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA
GCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAAC
AAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU

Sequence of entity 2 (AB, BB), FASTA

>4V9D_2 30S ribosomal protein S2 (chains AB, BB)
MLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKIL
FVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDK
LTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVD
TNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRS

Sequence of entity 3 (AC, BC), FASTA

>4V9D_3 30S ribosomal protein S3 (chains AC, BC)
GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPA
KSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSIT
SQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRAD
IDYNTSEAHTTYGVIGVKVWIFKGEI

Sequence of entity 4 (AD, BD), FASTA

>4V9D_4 30S ribosomal protein S4 (chains AD, BD)
ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKV
RRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHK
AIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGT
FKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE, BE), FASTA

>4V9D_5 30S ribosomal protein S5 (chains AE, BE)
ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARR
NMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYG
STNPINVVRATIDGLENMNSPEMVAAKRGK

Sequence of entity 6 (AF, BF), FASTA

>4V9D_6 30S ribosomal protein S6 (chains AF, BF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEAS

Sequence of entity 7 (AG, BG), FASTA

>4V9D_7 30S ribosomal protein S7 (chains AG, BG)
PRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEA
FEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLA
NELSDAAENKGTAVKKREDVHRMAEANKAFA

Sequence of entity 8 (AH, BH), FASTA

>4V9D_8 30S ribosomal protein S8 (chains AH, BH)
SMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELEL
TLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGL
GGEIICYVA

Sequence of entity 9 (AI, BI), FASTA

>4V9D_9 30S ribosomal protein S9 (chains AI, BI)
NQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDL
YITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARR
RPQFSKR

Sequence of entity 10 (AJ, BJ), FASTA

>4V9D_10 30S ribosomal protein S10 (chains AJ, BJ)
RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQ
YEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL

Sequence of entity 11 (AK, BK), FASTA

>4V9D_11 30S ribosomal protein S11 (chains AK, BK)
RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCAD
AVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV

Sequence of entity 12 (AL, BL), FASTA

>4V9D_12 30S ribosomal protein S12 (chains AL, BL)
ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGF
EVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKR
PKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	498
ZN	Zinc ion	Zn	2

Primary citation

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Dunkle, J.A., Wang, L., Feldman, M.B. et al. Science (2011) 332:981-984. DOI 10.1126/science.1202692 · PubMed

Other PDB entries of the same protein (UniProt P0A7V0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
4ODN 1.6 Å, Structure of SlyD from Thermus thermophilus in complex with S2-plus peptide
7OXH 1.7 Å, ttSlyD with pseudo-wild-type S2 peptide
4ODP 1.75 Å, Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide
4ODM 1.75 Å, Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide
8CGJ 1.79 Å, Streptomycin bound to the 30S body
8CF1 1.82 Å, Tetracycline bound to the 30S head
7OXJ 1.85 Å, ttSlyD with M8A pseudo-wild-type S2 peptide
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain

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4V9D is part of these collections:

The ribosome and protein synthesis

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