9FDA: E. coli 30S-IF1-IF3-mRNA-Edeine complex

Name: PDB 9FDA: Structure of E. coli 30S-IF1-IF3-mRNA-Edeine complex
Published: 2025-03-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Structure of E. coli 30S-IF1-IF3-mRNA-Edeine complex. Determined by electron microscopy at 2.0 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 2.0 Å
Organism: Escherichia coli
Chains: 15
Atoms: 36,060
Mol. weight: 688.06 kDa
Ligands: EDE, MG
Released: 19 Mar 2025

Explore 9FDA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FDA contains 60 α-helices and 67 β-strands across 14 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 D: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	28-30	3
α-helix	50-65	16
α-helix	69-81	13
α-helix	86-96	11
β-strand	97	1	1
α-helix	98-105	8
α-helix	111-119	9
β-strand	123-125	3	2
β-strand	128-129	2	2
β-strand	136	1	1
β-strand	141-145	5	2
α-helix	147-149	3
α-helix	153-164	12
α-helix	166-168	3
β-strand	171-174	4	2
β-strand	179-182	4	2
α-helix	185-187	3
α-helix	197-205	9

Chain E: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	12-24	13	3
β-strand	29-40	12	3
β-strand	45-53	9	3
α-helix	56-69	14
β-strand	72-73	2	3
β-strand	85-89	5	4
β-strand	92-98	7	4
β-strand	105-106	2	4
α-helix	110-118	9
β-strand	123-129	7	4
α-helix	133-145	13
α-helix	150-157	8
α-helix	161-164	4

Chain F: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	5
α-helix	12-14	3
α-helix	18-30	13
β-strand	35-51	17	5
β-strand	54-65	12	5
α-helix	68-80	13
β-strand	84-91	8	5
α-helix	99-100	2

Chain H: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-28	5	6
α-helix	31-43	13
β-strand	48-52	5	6
β-strand	58-62	5	6
β-strand	65-66	2	7
β-strand	69-70	2	7
β-strand	75-77	3	8
β-strand	80	1	9
β-strand	83	1	9
β-strand	86-87	2	8
α-helix	89-91	3
α-helix	92-94	3
α-helix	96-98	3
β-strand	101-106	6	8
β-strand	109-112	4	8
α-helix	113-119	7
β-strand	123-129	7	8

Chain I: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-17	10	10
β-strand	21-26	6	10
β-strand	31-36	6	10
α-helix	38-42	5
β-strand	52-58	7	10
β-strand	61-70	10	10

Chain J: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	79-86	8
β-strand	93-98	6	11
α-helix	104-119	16
β-strand	123-129	7	11
α-helix	134-137	4
α-helix	138-151	14
β-strand	156-158	3	11
β-strand	166	1	11
β-strand	169-176	8	11

Chain K: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	18-25	8	12
β-strand	30-35	6	12
β-strand	41-46	6	12
α-helix	60-71	12
β-strand	81-87	7	12
α-helix	94-102	9
β-strand	106-112	7	12
α-helix	131-137	7

Chain L: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-19	9
α-helix	22-24	3
β-strand	30-40	11	13
β-strand	50-57	8	13
β-strand	62-66	5	13
β-strand	79-84	6	13
β-strand	95-97	3	13
β-strand	101	1	14
β-strand	104	1	14
α-helix	105-107	3
α-helix	114-116	3

6 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
Small ribosomal subunit protein uS4	D	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
Small ribosomal subunit protein uS5	E	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
Small ribosomal subunit protein bS6, fully modified isoform	F	protein	135	Escherichia coli	P02358 (AlphaFold model)
Small ribosomal subunit protein uS8	H	protein	130	Escherichia coli	P0A7W7 (AlphaFold model)
Translation initiation factor IF-1	I	protein	72	Escherichia coli	P69222
Translation initiation factor IF-3	J	protein	180	Escherichia coli	P0A707
Small ribosomal subunit protein uS11	K	protein	139	Escherichia coli	P0A7R9
Small ribosomal subunit protein uS12	L	protein	124	Escherichia coli	P0A7S3
Small ribosomal subunit protein uS15	O	protein	89	Escherichia coli	P0ADZ4
Small ribosomal subunit protein bS16	P	protein	82	Escherichia coli	P0A7T3
Small ribosomal subunit protein uS17	Q	protein	84	Escherichia coli	P0AG63
Small ribosomal subunit protein bS18	R	protein	75	Escherichia coli	P0A7T7

3 more molecules are not listed.

Sequence of entity 1 (D), FASTA

>9FDA_1 Small ribosomal subunit protein uS4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 2 (E), FASTA

>9FDA_2 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 3 (F), FASTA

>9FDA_3 Small ribosomal subunit protein bS6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 4 (H), FASTA

>9FDA_4 Small ribosomal subunit protein uS8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 5 (I), FASTA

>9FDA_5 Translation initiation factor IF-1 (chains I)
MAKEDNIEMQGTVLETLPNTMFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVELTPY
DLSKGRIVFRSR

Sequence of entity 6 (J), FASTA

>9FDA_6 Translation initiation factor IF-3 (chains J)
MKGGKRVQTARPNRINGEIRAQEVRLTGLEGEQLGIVSLREALEKAEEAGVDLVEISPNA
EPPVCRIMDYGKFLYEKSKSSKEQKKKQKVIQVKEIKFRPGTDEGDYQVKLRSLIRFLEE
GDKAKITLRFRGREMAHQQIGMEVLNRVKDDLQELAVVESFPTKIEGRQMIMVLAPKKKQ

Sequence of entity 7 (K), FASTA

>9FDA_7 Small ribosomal subunit protein uS11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRVGCRPPKKRRV

Sequence of entity 8 (L), FASTA

>9FDA_8 Small ribosomal subunit protein uS12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Sequence of entity 9 (O), FASTA

>9FDA_9 Small ribosomal subunit protein uS15 (chains O)
MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMV
SQRRKLLDYLKRKDVARYTQLIERLGLRR

Sequence of entity 10 (P), FASTA

>9FDA_10 Small ribosomal subunit protein bS16 (chains P)
MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHW
VGQGATISDRVAALIKEVNKAA

Sequence of entity 11 (Q), FASTA

>9FDA_11 Small ribosomal subunit protein uS17 (chains Q)
MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVE
IRECRPLSKTKSWTLVRVVEKAVL

Sequence of entity 12 (R), FASTA

>9FDA_12 Small ribosomal subunit protein bS18 (chains R)
MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIK
RARYLSLLPYTDRHQ

Ligands and cofactors

ID	Name	Formula	Copies
EDE	Edeine B	C34 H59 N11 O10	1
MG	Magnesium ion	Mg	53

Water and common crystallization additives (K) are not listed.

Primary citation

The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation. Safdari, H.A., Morici, M., Sanchez-Castro, A. et al. Nat Commun (2025) 16:2470-2470. DOI 10.1038/s41467-025-57731-8 · PubMed

Other PDB entries of the same protein (UniProt P0A7V8 (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…
8CGJ 1.79 Å, Streptomycin bound to the 30S body
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
9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
8CGU 1.89 Å, Gentamicin bound to the 30S body
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA
7K00 1.98 Å, Structure of the Bacterial Ribosome at 2 Angstrom Resolution
9Q3R 1.99 Å, Cryo-EM structure of the Escherichia coli 70S ribosome bound to mRNA, P-site…

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