4WF1: E. coli ribosome

Crystal structure of the E. coli ribosome bound to negamycin. Determined by X-ray diffraction at 3.09 Å resolution. Released 5 Nov 2014.

Method: X-ray diffraction
Resolution: 3.09 Å
Organisms: Escherichia coli str. K-12 substr. MG1655, Escherichia coli, Thermus thermophilus
Chains: 105
Atoms: 288,204
Mol. weight: 4265.69 kDa
Ligands: NEG, ZN, MG
Released: 5 Nov 2014

Explore 4WF1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WF1 contains 454 α-helices and 635 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: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	31	1	8
β-strand	35	1	9
β-strand	38	1	9
α-helix	39-40	2
β-strand	41	1	8
α-helix	43-61	19
β-strand	69-70	2	10
α-helix	78-80	3
α-helix	83-86	4
β-strand	91-92	2	10
α-helix	104-106	3
α-helix	108-118	11
α-helix	135-145	11
α-helix	157-158	2
β-strand	162-163	2	10
α-helix	170-178	9
β-strand	184-186	3	10
β-strand	198-200	3	10
α-helix	207-209	3
α-helix	210-214	5
α-helix	215-221	7

Chain AC: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	20	1	16
α-helix	29-46	18
α-helix	47-50	4
β-strand	52-56	5	17
β-strand	57	1	16
β-strand	64	1	18
β-strand	67-70	4	17
α-helix	73-77	5
α-helix	82-95	14
β-strand	99	1	18
β-strand	105	1	17
α-helix	109-111	3
α-helix	113-124	12
α-helix	130-142	13
β-strand	148-152	5	19
β-strand	169-171	3	19
β-strand	182-191	10	19
β-strand	194-203	10	19

Chain AD: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	50-65	16
α-helix	69-81	13
α-helix	86-95	10
β-strand	97	1	32
α-helix	100-103	4
α-helix	111-119	9
β-strand	124	1	33
β-strand	129	1	33
β-strand	136	1	32
β-strand	141-142	2	34
β-strand	144	1	33
α-helix	153-162	10
β-strand	171-173	3	34
β-strand	180-182	3	34
α-helix	185-187	3
α-helix	197-203	7

Chain AE: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-22	10	42
β-strand	25	1	43
β-strand	28	1	43
β-strand	31-40	10	42
β-strand	46-49	4	42
β-strand	52-53	2	42
α-helix	56-68	13
β-strand	71-72	2	42
β-strand	77	1	44
β-strand	79-80	2	44
β-strand	85-89	5	45
β-strand	92-97	6	45
α-helix	112-116	5
β-strand	124-129	6	45
α-helix	133-146	14
α-helix	153-156	4

Chain AF: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	52
β-strand	7-10	4	52
α-helix	12-17	6
α-helix	18-30	13
β-strand	36-45	10	52
β-strand	57-66	10	52
α-helix	72-80	9
β-strand	84-86	3	52

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	23-30	8
α-helix	36-51	16
α-helix	59-68	10
β-strand	74-76	3	65
β-strand	87-89	3	65
α-helix	90-92	3
α-helix	93-109	17
α-helix	116-128	13
α-helix	133-147	15
α-helix	148-150	3

Chain AH: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-27	4	74
α-helix	31-42	12
β-strand	48-51	4	74
β-strand	59-62	4	74
β-strand	75-77	3	75
β-strand	80	1	76
β-strand	83	1	76
β-strand	86-87	2	75
β-strand	101-106	6	75
β-strand	109-112	4	75
α-helix	113-119	7
β-strand	123-129	7	75

Chain AI: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	82
β-strand	11-12	2	82
β-strand	15-22	8	82
β-strand	28-30	3	82
β-strand	34	1	82
α-helix	35-38	4
α-helix	45-48	4
α-helix	50-52	3
β-strand	62-68	7	82
α-helix	72-86	15
β-strand	120	1	83
β-strand	123	1	83

90 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, CA	RNA	1539	Escherichia coli str. K-12 substr. MG1655
30S ribosomal protein S2	AB, CB	protein	218	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	206	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	205	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	150	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	100	Escherichia coli	P02358
30S ribosomal protein S7	AG, CG	protein	151	Escherichia coli	P02359
30S ribosomal protein S8	AH, CH	protein	129	Escherichia coli	P0A7W7
30S ribosomal protein S9	AI, CI	protein	127	Escherichia coli	P0A7X3
30S ribosomal protein S10	AJ, CJ	protein	98	Escherichia coli	P0A7R5
30S ribosomal protein S11	AK, CK	protein	117	Escherichia coli	P0A7R9
30S ribosomal protein S12	AL, CL	protein	123	Escherichia coli	P0A7S3

41 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4WF1_1 16S rRNA (chains AA, CA)
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, CB), FASTA

>4WF1_2 30S ribosomal protein S2 (chains AB, CB)
MLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKIL
FVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDK
LTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVD
TNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRS

Sequence of entity 3 (AC, CC), FASTA

>4WF1_3 30S ribosomal protein S3 (chains AC, CC)
GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPA
KSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSIT
SQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRAD
IDYNTSEAHTTYGVIGVKVWIFKGEI

Sequence of entity 4 (AD, CD), FASTA

>4WF1_4 30S ribosomal protein S4 (chains AD, CD)
ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKV
RRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHK
AIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGT
FKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE, CE), FASTA

>4WF1_5 30S ribosomal protein S5 (chains AE, CE)
ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARR
NMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYG
STNPINVVRATIDGLENMNSPEMVAAKRGK

Sequence of entity 6 (AF, CF), FASTA

>4WF1_6 30S ribosomal protein S6 (chains AF, CF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEAS

Sequence of entity 7 (AG, CG), FASTA

>4WF1_7 30S ribosomal protein S7 (chains AG, CG)
PRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEA
FEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLA
NELSDAAENKGTAVKKREDVHRMAEANKAFA

Sequence of entity 8 (AH, CH), FASTA

>4WF1_8 30S ribosomal protein S8 (chains AH, CH)
SMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELEL
TLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGL
GGEIICYVA

Sequence of entity 9 (AI, CI), FASTA

>4WF1_9 30S ribosomal protein S9 (chains AI, CI)
NQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDL
YITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARR
RPQFSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4WF1_10 30S ribosomal protein S10 (chains AJ, CJ)
RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQ
YEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL

Sequence of entity 11 (AK, CK), FASTA

>4WF1_11 30S ribosomal protein S11 (chains AK, CK)
RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCAD
AVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV

Sequence of entity 12 (AL, CL), FASTA

>4WF1_12 30S ribosomal protein S12 (chains AL, CL)
ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGF
EVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKR
PKA

Ligands and cofactors

ID	Name	Formula	Copies
NEG	Negamycin	C9 H20 N4 O4	1
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	499

Primary citation

Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome. Olivier, N.B., Altman, R.B., Noeske, J. et al. Proc Natl Acad Sci U S A (2014) 111:16274-16279. DOI 10.1073/pnas.1414401111 · 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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