Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 24-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 953.59 kDa 
• Atom Count: 59062 
• Residue Count: 4732 
• Unique protein chains: 24
• Unique nucleic acid chains: 2

5ME1

Structure of the 30S Pre-Initiation Complex 2 (30S IC-2) Stalled by GE81112

• DOI: 10.2210/pdb5ME1/pdb
• EMDataResource: EMD-3495

• Classification: RIBOSOME
• Organism(s): Escherichia coli K-12, Thermus thermophilus HB8, Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-14 Released: 2017-01-11 
• Deposition Author(s): Lopez-Alonso, J.P., Fabbretti, A., Kaminishi, T., Iturrioz, I., Brandi, L., Gil Carton, D., Gualerzi, C., Fucini, P., Connell, S.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 13.5 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways.

Lopez-Alonso, J.P., Fabbretti, A., Kaminishi, T., Iturrioz, I., Brandi, L., Gil-Carton, D., Gualerzi, C.O., Fucini, P., Connell, S.R.

(2017) Nucleic Acids Res 45: 2179-2187

• PubMed: 27986852 
• DOI: 10.1093/nar/gkw1251
• Primary Citation of Related Structures:  
  5ME0, 5ME1


• PubMed Abstract: 
  

In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.

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Organizational Affiliation: 

IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B	241	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsB, b0169, JW0164
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Explore P0A7V0  Go to UniProtKB:  P0A7V0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C	233	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsC, b3314, JW3276
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Explore P0A7V3  Go to UniProtKB:  P0A7V3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D	206	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsD, ramA, b3296, JW3258
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Explore P0A7V8  Go to UniProtKB:  P0A7V8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	E	167	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsE, spc, b3303, JW3265
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Explore P0A7W1  Go to UniProtKB:  P0A7W1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	F	131	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsF, b4200, JW4158
Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358  Go to UniProtKB:  P02358

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G	156	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsG, b3341, JW3303
Find proteins for P02359 (Escherichia coli (strain K12)) Explore P02359  Go to UniProtKB:  P02359

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	H	130	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsH, b3306, JW3268
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7  Go to UniProtKB:  P0A7W7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I	130	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsI, b3230, JW3199
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Explore P0A7X3  Go to UniProtKB:  P0A7X3

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J	103	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsJ, nusE, b3321, JW3283
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Explore P0A7R5  Go to UniProtKB:  P0A7R5

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K	129	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsK, b3297, JW3259
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Explore P0A7R9  Go to UniProtKB:  P0A7R9

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L	123	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsL, strA, b3342, JW3304
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Explore P0A7S3  Go to UniProtKB:  P0A7S3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M	118	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsM, b3298, JW3260
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Explore P0A7S9  Go to UniProtKB:  P0A7S9

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	N	101	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsN, b3307, JW3269
Find proteins for P0AG59 (Escherichia coli (strain K12)) Explore P0AG59  Go to UniProtKB:  P0AG59

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O	89	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsO, secC, b3165, JW3134
Find proteins for P0ADZ4 (Escherichia coli (strain K12)) Explore P0ADZ4  Go to UniProtKB:  P0ADZ4

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P	102	Escherichia coli K-12	Mutation(s): 0
Find proteins for A0A0U4BH30 (Escherichia coli) Explore A0A0U4BH30  Go to UniProtKB:  A0A0U4BH30

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	Q	84	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsQ, neaA, b3311, JW3273
Find proteins for P0AG63 (Escherichia coli (strain K12)) Explore P0AG63  Go to UniProtKB:  P0AG63

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R	75	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsR, b4202, JW4160
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7  Go to UniProtKB:  P0A7T7

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	S	92	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsS, b3316, JW3278
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Explore P0A7U3  Go to UniProtKB:  P0A7U3

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	T	87	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsT, b0023, JW0022
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7  Go to UniProtKB:  P0A7U7

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	U	71	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpsU, b3065, JW3037
Find proteins for P68679 (Escherichia coli (strain K12)) Explore P68679  Go to UniProtKB:  P68679

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF-1	V	72	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: infA, TTHA1669
Find proteins for Q5SHR1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore Q5SHR1  Go to UniProtKB:  Q5SHR1

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF-2	W	890	Escherichia coli K-12	Mutation(s): 0  Gene Names: infB, gicD, ssyG, b3168, JW3137
Find proteins for P0A705 (Escherichia coli (strain K12)) Explore P0A705  Go to UniProtKB:  P0A705

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF-3	Y	171	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: infC
Find proteins for P03000 (Geobacillus stearothermophilus) Explore P03000  Go to UniProtKB:  P03000

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF-3	Z	144	Escherichia coli K-12	Mutation(s): 0  Gene Names: infC, fit, srjA, b1718, JW5829
Find proteins for P0A707 (Escherichia coli (strain K12)) Explore P0A707  Go to UniProtKB:  P0A707

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	A	1534	Escherichia coli K-12

Entity ID: 26
Molecule	Chains	Length	Organism	Image
fMet-tRNA	X	77	Escherichia coli K-12

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FME	X	N-FORMYLMETHIONINE C6 H11 N O3 S PYUSHNKNPOHWEZ-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
D2T	L	L-PEPTIDE LINKING	C5 H9 N O4 S		ASP

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 13.5 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-11-14 
• Released Date: 2017-01-11 
Deposition Author(s): Lopez-Alonso, J.P., Fabbretti, A., Kaminishi, T., Iturrioz, I., Brandi, L., Gil Carton, D., Gualerzi, C., Fucini, P., Connell, S.

Revision History 

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2018-10-24
  Changes: Advisory, Data collection, Derived calculations
• Version 1.4: 2018-11-21
  Changes: Advisory, Data collection, Derived calculations
• Version 1.5: 2019-10-23
  Changes: Data collection, Other
• Version 1.6: 2019-11-13
  Changes: Data collection, Other