6ZTJ: 30S ribosomal protein S2

E. coli 70S-RNAP expressome complex in NusG-coupled state (38 nt intervening mRNA). Determined by electron microscopy at 3.4 Å resolution. Released 16 Sept 2020.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Escherichia coli, synthetic construct
Chains: 66
Atoms: 176,970
Mol. weight: 2745.48 kDa
Ligands: MG, PHE, ZN
Released: 16 Sept 2020

Explore 6ZTJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZTJ contains 435 α-helices and 541 β-strands across 58 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16	1	3
α-helix	20-22	3
α-helix	25-27	3
β-strand	33-34	2	3
β-strand	39-40	2	3
α-helix	43-62	20
β-strand	67-70	4	4
α-helix	74-86	13
β-strand	90-92	3	4
α-helix	104-118	15
α-helix	119-124	6
α-helix	132-148	17
α-helix	151-153	3
β-strand	160-163	4	4
α-helix	170-179	10
β-strand	183-187	5	4
β-strand	198-201	4	4
α-helix	207-226	20

Chain AC: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	7-11	5
β-strand	12	1	15
β-strand	16	1	15
α-helix	17-18	2
α-helix	26-46	21
α-helix	48-50	3
β-strand	52-58	7	16
β-strand	64-70	7	16
α-helix	73-77	5
α-helix	82-95	14
β-strand	99-105	7	16
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-154	7	17
α-helix	157-159	3
β-strand	165-171	7	17
β-strand	180-191	12	17
β-strand	194-206	13	17

Chain AD: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	28-31	4
α-helix	37	1
α-helix	46-48	3
α-helix	51-65	15
α-helix	69-81	13
α-helix	86-96	11
β-strand	97	1	21
α-helix	98-105	8
α-helix	111-119	9
β-strand	123-125	3	22
β-strand	129	1	22
β-strand	136	1	21
β-strand	141-145	5	22
α-helix	147-150	4
α-helix	153-164	12
α-helix	166-168	3
β-strand	171-174	4	22
β-strand	179-182	4	22
α-helix	185-187	3
α-helix	198-203	6

Chain AE: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	26
β-strand	31-40	10	26
β-strand	46-49	4	26
β-strand	52-53	2	26
α-helix	56-68	13
β-strand	72	1	26
β-strand	77	1	27
β-strand	80	1	27
β-strand	85-88	4	28
β-strand	92-97	6	28
α-helix	99-100	2
β-strand	105-106	2	28
α-helix	109-118	10
β-strand	122	1	27
β-strand	123-129	7	28
α-helix	133-145	13
α-helix	150-157	8
α-helix	161-164	4

Chain AF: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	33
α-helix	12-17	6
α-helix	18-31	14
β-strand	35-45	11	33
β-strand	51	1	34
β-strand	54	1	34
β-strand	57-66	10	33
α-helix	68-80	13
β-strand	84-92	9	33

Chain AG: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	13-15	3
α-helix	21-30	10
α-helix	36-54	19
α-helix	58-69	12
β-strand	73-78	6	40
α-helix	84	1
β-strand	85-90	6	40
α-helix	91-92	2
α-helix	93-110	18
α-helix	116-129	14
α-helix	133-147	15
α-helix	149-151	3

Chain AH: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-20	15
β-strand	24-28	5	44
α-helix	31-43	13
β-strand	46-52	7	44
β-strand	58-63	6	44
β-strand	65	1	45
β-strand	70	1	45
β-strand	75-77	3	46
β-strand	80	1	47
β-strand	83	1	47
β-strand	86-87	2	46
α-helix	89-91	3
α-helix	95-98	4
β-strand	101-106	6	46
β-strand	109-112	4	46
α-helix	113-119	7
β-strand	123-129	7	46

Chain AI: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	48
β-strand	15-23	9	48
β-strand	28-30	3	48
β-strand	34	1	48
α-helix	35-38	4
α-helix	42-54	13
α-helix	58-60	3
β-strand	61-68	8	48
α-helix	72-90	19
α-helix	95-101	7
α-helix	112-114	3
α-helix	124-127	4

50 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	RNA	1542	Escherichia coli
30S ribosomal protein S2	AB	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF	protein	131	Escherichia coli	P02358
30S ribosomal protein S7	AG	protein	156	Escherichia coli	P02359
30S ribosomal protein S8	AH	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	AI	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	AJ	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	AK	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	AL	protein	124	Escherichia coli	P0A7S3

53 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>6ZTJ_1 16S ribosomal RNA (chains AA)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGCAGCUUGCUGCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Sequence of entity 2 (AB), FASTA

>6ZTJ_2 30S ribosomal protein S2 (chains AB)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (AC), FASTA

>6ZTJ_3 30S ribosomal protein S3 (chains AC)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (AD), FASTA

>6ZTJ_4 30S ribosomal protein S4 (chains AD)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE), FASTA

>6ZTJ_5 30S ribosomal protein S5 (chains AE)
MAHIEKQACELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPAMVAAKRGKSVEEILGK

Sequence of entity 6 (AF), FASTA

>6ZTJ_6 30S ribosomal protein S6 (chains AF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDADAGDSEE

Sequence of entity 7 (AG), FASTA

>6ZTJ_7 30S ribosomal protein S7 (chains AG)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW

Sequence of entity 8 (AH), FASTA

>6ZTJ_8 30S ribosomal protein S8 (chains AH)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (AI), FASTA

>6ZTJ_9 30S ribosomal protein S9 (chains AI)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (AJ), FASTA

>6ZTJ_10 30S ribosomal protein S10 (chains AJ)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (AK), FASTA

>6ZTJ_11 30S ribosomal protein S11 (chains AK)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 12 (AL), FASTA

>6ZTJ_12 30S ribosomal protein S12 (chains AL)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	479
PHE	Phenylalanine	C9 H11 N O2	1
ZN	Zinc ion	Zn	4

Primary citation

Structural basis of transcription-translation coupling and collision in bacteria. Webster, M.W., Takacs, M., Zhu, C. et al. Science (2020) 369:1355-1359. DOI 10.1126/science.abb5036 · 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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