8YDI | pdb_00008ydi

E.coli transcription translation coupling complex in TTC-P state 1 (subclass 2) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin

• PDB DOI: https://doi.org/10.2210/pdb8YDI/pdb
• NAKB: 8YDI
• EM Map EMD-39172: EMDB EMDataResource

• Classification: RIBOSOME
• Organism(s): Escherichia coli K-12, synthetic construct, Streptomyces
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-20 Released: 2025-08-27 
• Deposition Author(s): Zhang, J., Lu, G., Wang, C., Lin, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

E.coli transcription translation coupling complex in TTC-P state 1 (subclass 2) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin

Zhang, J., Lu, G., Ebright, R.H., Lin, J., Wang, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 58-mer - AA2AB1AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 58-mer - AA2AB2AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,735.05 kDa 
• Atom Count: 178,130 
• Modeled Residue Count: 14,592 
• Deposited Residue Count: 15,161 
• Unique protein chains: 57
• Unique nucleic acid chains: 8

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	A	70	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	B	57	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4  Go to UniProtKB:  P0A7N4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	C	55	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Explore P0A7N9  Go to UniProtKB:  P0A7N9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	D	46	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5  Go to UniProtKB:  P0A7P5

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	E	65	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1  Go to UniProtKB:  P0A7Q1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	F	38	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Explore P0A7Q6  Go to UniProtKB:  P0A7Q6

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	G	241	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Explore P0A7V0  Go to UniProtKB:  P0A7V0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	H	233	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Explore P0A7V3  Go to UniProtKB:  P0A7V3

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	I	206	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Explore P0A7V8  Go to UniProtKB:  P0A7V8

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	J	167	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Explore P0A7W1  Go to UniProtKB:  P0A7W1

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6, fully modified isoform	K	135	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358  Go to UniProtKB:  P02358

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	L	179	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P02359 (Escherichia coli (strain K12)) Explore P02359  Go to UniProtKB:  P02359

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	M	130	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7  Go to UniProtKB:  P0A7W7

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	N	130	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Explore P0A7X3  Go to UniProtKB:  P0A7X3

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	O	103	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Explore P0A7R5  Go to UniProtKB:  P0A7R5

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	P	129	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Explore P0A7R9  Go to UniProtKB:  P0A7R9

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	Q	124	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Explore P0A7S3  Go to UniProtKB:  P0A7S3

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	R	118	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Explore P0A7S9  Go to UniProtKB:  P0A7S9

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	S	101	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12)) Explore P0AG59  Go to UniProtKB:  P0AG59

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	T	89	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12)) Explore P0ADZ4  Go to UniProtKB:  P0ADZ4

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	U	82	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Explore P0A7T3  Go to UniProtKB:  P0A7T3

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	V	84	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12)) Explore P0AG63  Go to UniProtKB:  P0AG63

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	W	75	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7  Go to UniProtKB:  P0A7T7

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	X	92	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Explore P0A7U3  Go to UniProtKB:  P0A7U3

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	Y	87	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7  Go to UniProtKB:  P0A7U7

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	Z	71	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P68679 (Escherichia coli (strain K12)) Explore P68679  Go to UniProtKB:  P68679

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	AA [auth b]	273	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	BA [auth c]	209	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438  Go to UniProtKB:  P60438

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	CA [auth d]	201	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723  Go to UniProtKB:  P60723

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	DA [auth e]	179	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P62399 (Escherichia coli (strain K12)) Explore P62399  Go to UniProtKB:  P62399

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	EA [auth f]	177	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12)) Explore P0AG55  Go to UniProtKB:  P0AG55

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	FA [auth g]	149	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1  Go to UniProtKB:  P0A7R1

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	GA [auth i]	142	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	HA [auth j]	142	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10  Go to UniProtKB:  P0AA10

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	IA [auth k]	123	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3  Go to UniProtKB:  P0ADY3

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	JA [auth l]	144	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413  Go to UniProtKB:  P02413

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	KA [auth m]	136	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Explore P0ADY7  Go to UniProtKB:  P0ADY7

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	LA [auth n]	127	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44  Go to UniProtKB:  P0AG44

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	MA [auth o]	117	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018  Go to UniProtKB:  P0C018

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	NA [auth p]	115	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	OA [auth q]	118	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3  Go to UniProtKB:  P0A7L3

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	PA [auth r]	103	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48  Go to UniProtKB:  P0AG48

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	QA [auth s]	110	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175  Go to UniProtKB:  P61175

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	RA [auth t]	100	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0  Go to UniProtKB:  P0ADZ0

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	SA [auth u]	104	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624  Go to UniProtKB:  P60624

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	TA [auth v]	94	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919  Go to UniProtKB:  P68919

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	UA [auth w]	85	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8  Go to UniProtKB:  P0A7L8

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	VA [auth x]	78	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Explore P0A7M2  Go to UniProtKB:  P0A7M2

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	WA [auth y]	63	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	XA [auth z]	59	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51  Go to UniProtKB:  P0AG51

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	EB [auth A1], FB [auth A2]	329	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoA EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4  Go to UniProtKB:  P0A7Z4

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	GB [auth B1]	1,407	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoC EC: 2.7.7.6
UniProt
Find proteins for P0A7K2 (Escherichia coli (strain K12)) Explore P0A7K2  Go to UniProtKB:  P0A7K2

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	HB [auth B2]	1,342	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 EC: 2.7.7.6
UniProt
Find proteins for P0A7K2 (Escherichia coli (strain K12)) Explore P0A7K2  Go to UniProtKB:  P0A7K2

Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	IB [auth W0]	91	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800  Go to UniProtKB:  P0A800

Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination/antitermination protein NusA	JB [auth NA]	495	Escherichia coli K-12	Mutation(s): 0  Gene Names: nusA, b3169, JW3138
UniProt
Find proteins for P0AFF6 (Escherichia coli (strain K12)) Explore P0AFF6  Go to UniProtKB:  P0AFF6

Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination/antitermination protein NusG	KB [auth NG]	181	Escherichia coli K-12	Mutation(s): 0  Gene Names: nusG, b3982, JW3945
UniProt
Find proteins for P0AFG0 (Escherichia coli (strain K12)) Explore P0AFG0  Go to UniProtKB:  P0AFG0

Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
viomycin	OB [auth h]	6	Streptomyces	Mutation(s): 0

Entity ID: 51
Molecule	Chains	Length	Organism	Image
23S rRNA	YA [auth 1]	2,904	Escherichia coli K-12

Entity ID: 52
Molecule	Chains	Length	Organism	Image
5S rRNA	ZA [auth 2]	120	Escherichia coli K-12

Entity ID: 53
Molecule	Chains	Length	Organism	Image
16S rRNA	AB [auth 3]	1,542	Escherichia coli K-12

Entity ID: 54
Molecule	Chains	Length	Organism	Image
mRNA	BB [auth 4]	56	synthetic construct

Entity ID: 55
Molecule	Chains	Length	Organism	Image
templete DNA strand	CB [auth 8]	37	synthetic construct

Entity ID: 56
Molecule	Chains	Length	Organism	Image
non-templete DNA strand	DB [auth 9]	37	synthetic construct

Entity ID: 63
Molecule	Chains	Length	Organism	Image
tRNA(Phe)	LB [auth 5]	76	Escherichia coli K-12

Entity ID: 64
Molecule	Chains	Length	Organism	Image
tRNA(fMet)	MB [auth 6], NB [auth 7]	77	Escherichia coli K-12

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	PB [auth B1]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5OH	OB [auth h]	L-PEPTIDE LINKING	C6 H12 N4 O3		ALA
DPP	OB [auth h]	L-PEPTIDE LINKING	C3 H8 N2 O2		ALA
KBE	OB [auth h]	L-PEPTIDE LINKING	C6 H14 N2 O2		LYS
UAL	OB [auth h]	PEPTIDE LINKING	C4 H7 N3 O3		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 65
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000226	OB [auth h]	Viomycin	Oligopeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Zhang, J., Lu, G., Wang, C., Lin, J.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32270039
National Natural Science Foundation of China (NSFC)	China	32130063

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release