7UG7: 30S ribosomal protein S2

Name: PDB 7UG7: 70S ribosome complex in an intermediate state of translocation bound to EF-G(GDP) stalled by Argyrin B
Published: 2022-05-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

70S ribosome complex in an intermediate state of translocation bound to EF-G(GDP) stalled by Argyrin B. Determined by electron microscopy at 2.58 Å resolution. Released 18 May 2022.

Method: Electron microscopy
Resolution: 2.58 Å
Organisms: Escherichia coli, Escherichia coli K-12, Actinoplanes sp.
Chains: 60
Atoms: 154,353
Mol. weight: 2354.27 kDa
Ligands: PUT, MG, SPD, ZN
Released: 18 May 2022

Explore 7UG7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UG7 contains 289 α-helices and 381 β-strands across 53 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 EF: 31 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	23
α-helix	23-37	15
β-strand	67-72	6	23
α-helix	80-81	2
β-strand	82-88	7	23
α-helix	93-95	3
α-helix	96-105	10
β-strand	109-114	6	23
β-strand	118	1	23
α-helix	121-132	12
β-strand	137-142	6	23
α-helix	151-161	11
β-strand	165-168	4	23
β-strand	170-171	2	24
α-helix	176-178	3
β-strand	182-184	3	24
β-strand	189-191	3	24
β-strand	204-205	2	24
α-helix	206-208	3
α-helix	209-230	22
α-helix	232-239	8
α-helix	241-244	4
α-helix	245-258	14
β-strand	261-266	6	23
β-strand	268	1	25
β-strand	273	1	25
α-helix	275-285	11
α-helix	293-295	3
β-strand	297-299	3	26
β-strand	306	1	26
β-strand	318-325	8	27
α-helix	331-332	2
β-strand	333-340	8	27
β-strand	343-344	2	28
β-strand	347-351	5	27
β-strand	356-360	5	27
β-strand	363-366	4	27
β-strand	367	1	23
β-strand	371-374	4	27
β-strand	376-377	2	28
β-strand	381-386	6	27
α-helix	395	1
β-strand	396-398	3	27
β-strand	404-406	3	26
α-helix	407-410	4
α-helix	412-414	3
β-strand	416-422	7	29
α-helix	427-441	15
β-strand	446-449	4	29
β-strand	456-460	5	29
α-helix	463-475	13
β-strand	481-484	4	29
α-helix	485-488	4
β-strand	491-495	5	30
β-strand	498-506	9	31
β-strand	515-523	9	31
α-helix	524-526	3
β-strand	534-538	5	31
α-helix	549-562	14
α-helix	569-570	2
β-strand	571	1	30
β-strand	574-582	9	31
α-helix	590-607	18
β-strand	609-613	5	30
β-strand	616-623	8	32
α-helix	625-627	3
α-helix	628-637	10
β-strand	641-647	7	32
β-strand	652-659	8	32
α-helix	666-674	9
β-strand	679-686	8	32
α-helix	688	1
β-strand	689	1	30
α-helix	690-691	2
α-helix	692-699	8

Chain La: 0 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	91
β-strand	30-31	2	92
β-strand	36-39	4	91
β-strand	45-47	3	92
β-strand	51-53	3	91
β-strand	59-61	3	91
β-strand	65-72	8	92
β-strand	77-84	8	92

Chain LA: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
α-helix	23-32	10
β-strand	41	1	96
β-strand	43-44	2	97
β-strand	46-48	3	98
α-helix	55-57	3
β-strand	60-64	5	99
β-strand	160-164	5	99
β-strand	170-171	2	98
β-strand	177	1	96
α-helix	182-199	18
β-strand	209-211	3	98
β-strand	213-215	3	97
α-helix	219-221	3
β-strand	222-223	2	97

Chain Lb: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	93
β-strand	24-29	6	93
β-strand	33-40	8	94
β-strand	45-52	8	94
α-helix	53-62	10
α-helix	64-74	11

Chain LB: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	101
α-helix	13-15	3
β-strand	17-19	3	101
β-strand	24	1	102
β-strand	34-36	3	103
β-strand	43	1	104
β-strand	49	1	104
β-strand	54	1	105
β-strand	61-63	3	103
β-strand	65	1	102
β-strand	76-82	7	102
β-strand	91-96	6	102
β-strand	101-105	5	102
β-strand	107	1	106
β-strand	115-116	2	102
β-strand	118	1	107
β-strand	129-131	3	107
α-helix	136	1
β-strand	140-142	3	107
β-strand	144	1	108
β-strand	154	1	108
β-strand	162-168	7	107
β-strand	171-175	5	107
β-strand	181-185	5	107
β-strand	189-192	4	107
β-strand	195	1	106
α-helix	198-202	5
β-strand	204	1	101
α-helix	208-213	6
β-strand	216	1	105
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	109
β-strand	251	1	109
β-strand	267-269	3	107

Chain Lc: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-34	24
α-helix	41-60	20

Chain LC: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	112
β-strand	21-28	8	112
β-strand	32-38	7	113
β-strand	47-52	6	113
α-helix	57-59	3
α-helix	62-71	10
β-strand	78-83	6	113
α-helix	84-85	2
β-strand	95-96	2	113
α-helix	98-101	4
β-strand	106-112	7	112
α-helix	113-115	3
β-strand	117-119	3	114
α-helix	121-125	5
α-helix	127-129	3
β-strand	149	1	115
β-strand	152	1	115
α-helix	155-156	2
β-strand	163-165	3	114
β-strand	169-181	13	112
β-strand	186-190	5	112
β-strand	200-205	6	112

Chain Ld: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	95
α-helix	18-27	10
β-strand	35-39	5	95
α-helix	42-50	9
β-strand	55-58	4	95

45 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	16	RNA	1534	Escherichia coli
30S ribosomal protein S2	SB	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	SC	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	SD	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	SE	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	SF	protein	135	Escherichia coli	P02358
30S ribosomal protein S7	SG	protein	179	Escherichia coli	P02359
30S ribosomal protein S8	SH	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	SI	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	SJ	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	SK	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	SL	protein	124	Escherichia coli	P0A7S3

48 more molecules are not listed.

Sequence of entity 1 (16), FASTA

>7UG7_1 16S rRNA (chains 16)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA

Sequence of entity 2 (SB), FASTA

>7UG7_2 30S ribosomal protein S2 (chains SB)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFEKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (SC), FASTA

>7UG7_3 30S ribosomal protein S3 (chains SC)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (SD), FASTA

>7UG7_4 30S ribosomal protein S4 (chains SD)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (SE), FASTA

>7UG7_5 30S ribosomal protein S5 (chains SE)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (SF), FASTA

>7UG7_6 30S ribosomal protein S6 (chains SF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (SG), FASTA

>7UG7_7 30S ribosomal protein S7 (chains SG)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (SH), FASTA

>7UG7_8 30S ribosomal protein S8 (chains SH)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (SI), FASTA

>7UG7_9 30S ribosomal protein S9 (chains SI)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (SJ), FASTA

>7UG7_10 30S ribosomal protein S10 (chains SJ)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (SK), FASTA

>7UG7_11 30S ribosomal protein S11 (chains SK)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 12 (SL), FASTA

>7UG7_12 30S ribosomal protein S12 (chains SL)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
PUT	1,4-diaminobutane	C4 H12 N2	11
MG	Magnesium ion	Mg	404
SPD	Spermidine	C7 H19 N3	2
ZN	Zinc ion	Zn	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
FME	N-formylmethionine	C6 H11 N O3 S	1
PHE	Phenylalanine	C9 H11 N O2	1

Primary citation

The cyclic octapeptide antibiotic argyrin B inhibits translation by trapping EF-G on the ribosome during translocation. Wieland, M., Holm, M., Rundlet, E.J. et al. Proc Natl Acad Sci U S A (2022) 119:e2114214119-e2114214119. DOI 10.1073/pnas.2114214119 · 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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