5AFI: 30S ribosomal protein S2

Name: PDB 5AFI: 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM
Published: 2015-03-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM. Determined by electron microscopy at 2.9 Å resolution. Released 11 Mar 2015.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Escherichia coli
Chains: 59
Atoms: 152,717
Mol. weight: 2302.71 kDa
Ligands: ZN, GDP, KIR, FME
Released: 11 Mar 2015

Explore 5AFI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AFI contains 257 α-helices and 395 β-strands across 52 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 0: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	16-18	3
β-strand	28-29	2	1
β-strand	36-37	2	1
β-strand	41	1	90
β-strand	48	1	2
β-strand	51	1	2

Chain 1: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	5
β-strand	19-24	6	5
α-helix	32-33	2
β-strand	48-51	4	5

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-22	5
α-helix	25-36	12

Chain 3: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	9-11	3
β-strand	14-15	2	23
β-strand	21-23	3	23
α-helix	37-42	6
β-strand	47-48	2	23
α-helix	49-50	2
α-helix	51-60	10

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	35
β-strand	14-17	4	35
α-helix	19-21	3
β-strand	24-27	4	35
β-strand	35	1	35

Chain 5: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	4-19	16
α-helix	34-47	14
α-helix	64-66	3
α-helix	72-77	6
α-helix	97-103	7
α-helix	111-113	3

Chain 6: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	50
β-strand	21-25	5	50
β-strand	32-34	3	50
α-helix	46-51	6
α-helix	57-64	8

Chain b: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	3
β-strand	32-33	2	3
β-strand	37-39	3	3
α-helix	45-61	17
β-strand	66-69	4	4
α-helix	74-84	11
β-strand	89-91	3	4
α-helix	103-121	19
α-helix	130-146	17
β-strand	159-162	4	4
α-helix	169-175	7
β-strand	184-186	3	4
β-strand	198-200	3	4
α-helix	206-221	16

44 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	a	RNA	1539	Escherichia coli
30S ribosomal protein S2	b	protein	240	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	c	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	d	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	e	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	f	protein	135	Escherichia coli	P02358
30S ribosomal protein S7	g	protein	179	Escherichia coli	P02359
30S ribosomal protein S8	h	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	i	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	j	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	k	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	l	protein	124	Escherichia coli	P0A7S3

46 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>5AFI_1 16S ribosomal RNA (chains a)
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 (b), FASTA

>5AFI_2 30S ribosomal protein S2 (chains b)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA

Sequence of entity 3 (c), FASTA

>5AFI_3 30S ribosomal protein S3 (chains c)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (d), FASTA

>5AFI_4 30S ribosomal protein S4 (chains d)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (e), FASTA

>5AFI_5 30S ribosomal protein S5 (chains e)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (f), FASTA

>5AFI_6 30S ribosomal protein S6 (chains f)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (g), FASTA

>5AFI_7 30S ribosomal protein S7 (chains g)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (h), FASTA

>5AFI_8 30S ribosomal protein S8 (chains h)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (i), FASTA

>5AFI_9 30S ribosomal protein S9 (chains i)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (j), FASTA

>5AFI_10 30S ribosomal protein S10 (chains j)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (k), FASTA

>5AFI_11 30S ribosomal protein S11 (chains k)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 12 (l), FASTA

>5AFI_12 30S ribosomal protein S12 (chains l)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
KIR	Kirromycin	C43 H60 N2 O12	1
FME	N-formylmethionine	C6 H11 N O3 S	1
MG	Magnesium ion	Mg	333

Water and common crystallization additives (NA, CL) are not listed.

Primary citation

Structure of the E. coli ribosome-EF-Tu complex at <3 angstrom resolution by Cs-corrected cryo-EM. Fischer, N., Neumann, P., Konevega, A.L. et al. Nature (2015) 520:567-570. DOI 10.1038/nature14275 · 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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