4YBB: Escherichia coli ribosome

Name: PDB 4YBB: High-resolution structure of the Escherichia coli ribosome
Published: 2015-03-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

High-resolution structure of the Escherichia coli ribosome. Determined by X-ray diffraction at 2.1 Å resolution. Released 18 Mar 2015.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Escherichia coli K-12, Escherichia coli (strain K12), Escherichia coli
Chains: 105
Atoms: 295,060
Mol. weight: 4270.48 kDa
Ligands: MG, PUT, ZN, SPD
Released: 18 Mar 2015

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

Secondary structure: helices and β-sheets

4YBB contains 515 α-helices and 636 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	9
α-helix	20-22	3
α-helix	25-27	3
β-strand	31-35	5	9
β-strand	38-41	4	9
α-helix	43-62	20
β-strand	67-70	4	10
α-helix	77-85	9
β-strand	90-92	3	10
α-helix	96-97	2
α-helix	104-122	19
α-helix	133-148	16
β-strand	160-164	5	10
α-helix	170-179	10
β-strand	183-186	4	10
α-helix	193-195	3
β-strand	198-200	3	10
α-helix	207-226	20

Chain AC: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	12	1	18
β-strand	16	1	18
β-strand	20	1	19
α-helix	26-46	21
β-strand	52-58	7	19
β-strand	64-70	7	19
α-helix	73-77	5
α-helix	79-81	3
α-helix	82-95	14
β-strand	99-105	7	19
α-helix	109-111	3
α-helix	113-126	14
α-helix	130-143	14
β-strand	148-154	7	20
α-helix	157-159	3
β-strand	165-171	7	20
β-strand	182-191	10	20
β-strand	194-203	10	20

Chain AD: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	28-30	3
α-helix	50-65	16
α-helix	69-81	13
α-helix	86-95	10
β-strand	97	1	34
α-helix	98-104	7
α-helix	111-119	9
β-strand	123-125	3	35
β-strand	128-129	2	35
α-helix	135	1
β-strand	136	1	34
α-helix	137	1
β-strand	141-145	5	35
α-helix	147-149	3
α-helix	153-164	12
α-helix	166-168	3
β-strand	171-174	4	35
β-strand	179-182	4	35
α-helix	188-190	3
α-helix	197-203	7

Chain AE: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-25	14	41
β-strand	28-40	13	41
β-strand	45-53	9	41
α-helix	56-68	13
β-strand	71-73	3	41
β-strand	77	1	42
β-strand	80	1	42
β-strand	85-89	5	43
β-strand	92-98	7	43
β-strand	105-106	2	43
α-helix	109-118	10
β-strand	123-129	7	43
α-helix	133-145	13
α-helix	150-157	8

Chain AF: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	50
α-helix	12-17	6
α-helix	18-31	14
β-strand	35-45	11	50
β-strand	51	1	51
β-strand	54	1	51
β-strand	57-65	9	50
α-helix	68-80	13
β-strand	84-92	9	50
α-helix	101-105	5

Chain AG: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	21-30	10
α-helix	36-52	17
α-helix	58-69	12
β-strand	73-79	7	57
β-strand	84-90	7	57
α-helix	91-92	2
α-helix	93-109	17
α-helix	116-128	13
α-helix	133-147	15
α-helix	149-151	3

Chain AH: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-28	5	64
α-helix	31-42	12
β-strand	48-52	5	64
α-helix	57	1
β-strand	58-62	5	64
β-strand	65	1	65
β-strand	70	1	65
β-strand	75-77	3	66
β-strand	80	1	67
β-strand	83	1	67
β-strand	86-87	2	66
α-helix	89-91	3
α-helix	95-98	4
β-strand	101-106	6	66
β-strand	109-112	4	66
α-helix	113-118	6
β-strand	123-129	7	66

Chain AI: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	73
β-strand	15-23	9	73
β-strand	25	1	74
β-strand	28-30	3	73
β-strand	33-34	2	73
α-helix	35-38	4
α-helix	42-49	8
β-strand	60	1	74
β-strand	61-68	8	73
α-helix	72-90	19
α-helix	95-101	7
α-helix	110-114	5
α-helix	123-126	4

81 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	1534	Escherichia coli K-12
30S ribosomal protein S2	AB, BB	protein	224	Escherichia coli (strain K12)	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC, BC	protein	206	Escherichia coli (strain K12)	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD, BD	protein	205	Escherichia coli (strain K12)	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE, BE	protein	155	Escherichia coli (strain K12)	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF, BF	protein	106	Escherichia coli (strain K12)	P02358
30S ribosomal protein S7	AG, BG	protein	151	Escherichia coli (strain K12)	P02359
30S ribosomal protein S8	AH, BH	protein	129	Escherichia coli (strain K12)	P0A7W7
30S ribosomal protein S9	AI, BI	protein	127	Escherichia coli (strain K12)	P0A7X3
30S ribosomal protein S10	AJ, BJ	protein	99	Escherichia coli (strain K12)	P0A7R5
30S ribosomal protein S11	AK, BK	protein	117	Escherichia coli (strain K12)	P0A7R9
30S ribosomal protein S12	AL, BL	protein	123	Escherichia coli (strain K12)	P0A7S3

43 more molecules are not listed.

Sequence of entity 1 (AA, BA), FASTA

>4YBB_1 16S rRNA (chains AA, BA)
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 (AB, BB), FASTA

>4YBB_2 30S ribosomal protein S2 (chains AB, BB)
VSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASR
KGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQD
GTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPV
FAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQ

Sequence of entity 3 (AC, BC), FASTA

>4YBB_3 30S ribosomal protein S3 (chains AC, BC)
GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPA
KSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSIT
SQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRAD
IDYNTSEAHTTYGVIGVKVWIFKGEI

Sequence of entity 4 (AD, BD), FASTA

>4YBB_4 30S ribosomal protein S4 (chains AD, BD)
ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKV
RRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHK
AIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGT
FKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE, BE), FASTA

>4YBB_5 30S ribosomal protein S5 (chains AE, BE)
ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARR
NMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYG
STNPINVVRATIDGLENMNSPEMVAAKRGKSVEEI

Sequence of entity 6 (AF, BF), FASTA

>4YBB_6 30S ribosomal protein S6 (chains AF, BF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAK

Sequence of entity 7 (AG, BG), FASTA

>4YBB_7 30S ribosomal protein S7 (chains AG, BG)
PRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEA
FEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLA
NELSDAAENKGTAVKKREDVHRMAEANKAFA

Sequence of entity 8 (AH, BH), FASTA

>4YBB_8 30S ribosomal protein S8 (chains AH, BH)
SMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELEL
TLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGL
GGEIICYVA

Sequence of entity 9 (AI, BI), FASTA

>4YBB_9 30S ribosomal protein S9 (chains AI, BI)
NQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDL
YITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARR
RPQFSKR

Sequence of entity 10 (AJ, BJ), FASTA

>4YBB_10 30S ribosomal protein S10 (chains AJ, BJ)
QRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARD
QYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL

Sequence of entity 11 (AK, BK), FASTA

>4YBB_11 30S ribosomal protein S11 (chains AK, BK)
RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCAD
AVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV

Sequence of entity 12 (AL, BL), FASTA

>4YBB_12 30S ribosomal protein S12 (chains AL, BL)
ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGF
EVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVKR
PKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	463
PUT	1,4-diaminobutane	C4 H12 N2	16
ZN	Zinc ion	Zn	3
SPD	Spermidine	C7 H19 N3	4
GUN	Guanine	C5 H5 N5 O	1

Water and common crystallization additives (PG4, MPD, PEG, 1PE, PGE, ACY, EDO, TRS) are not listed.

Primary citation

High-resolution structure of the Escherichia coli ribosome. Noeske, J., Wasserman, M.R., Terry, D.S. et al. Nat Struct Mol Biol (2015) 22:336-341. DOI 10.1038/nsmb.2994 · 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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