9L0Y | pdb_00009l0y

Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu middle transcription activator Mor

• PDB DOI: https://doi.org/10.2210/pdb9L0Y/pdb
• NAKB: 9L0Y
• EM Map EMD-62728: EMDB EMDataResource

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia phage Mu, Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-13 Released: 2025-12-17 
• Deposition Author(s): Lin, W., Feng, Y., Shi, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu middle transcription activator Mor

Lin, W., Shi, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 11-mer - A4B2C1D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 11-mer - A2B2C2D1E1F1G1H1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 602.41 kDa 
• Atom Count: 35,859 
• Modeled Residue Count: 4,332 
• Deposited Residue Count: 5,108 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	C [auth A], D [auth B], M [auth P]	329	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoA, pez, phs, sez, b3295, JW3257 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4  Go to UniProtKB:  P0A7Z4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	E [auth C]	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 P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2  Go to UniProtKB:  P0A8V2

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	F [auth D]	1,407	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoC, tabB, b3988, JW3951 EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7  Go to UniProtKB:  P0A8T7

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	G [auth E]	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor RpoD	H [auth F]	613	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoD, alt, b3067, JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12)) Explore P00579  Go to UniProtKB:  P00579

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Middle operon regulator	I [auth G], J, K [auth M], L [auth N]	129	Escherichia phage Mu	Mutation(s): 0  Gene Names: mor, Mup17
UniProt
Find proteins for P23848 (Escherichia phage Mu) Explore P23848  Go to UniProtKB:  P23848

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (76-MER)	A [auth 1]	76	Escherichia phage Mu

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (76-MER)	B [auth 2]	76	Escherichia phage Mu

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Lin, W., Feng, Y., Shi, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81903526

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release