9N11 | pdb_00009n11

Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state

• PDB DOI: https://doi.org/10.2210/pdb9N11/pdb
• EM Map EMD-48802: EMDB EMDataResource
• NAKB: 9N11

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-24 Released: 2025-10-15 
• Deposition Author(s): Brewer, J.J., Darst, S.A., Campbell, E.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state

Brewer, J.J., Darst, S.A., Campbell, E.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 541.32 kDa 
• Atom Count: 35,717 
• Modeled Residue Count: 4,374 
• Deposited Residue Count: 4,571 
• Unique protein chains: 5
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription-repair-coupling factor	A	1,166	Escherichia coli	Mutation(s): 0  Gene Names:  mfd, ACU57_04350, BGM66_002106, CTR35_002399, E4K51_18465, EIZ93_13025, FOI11_007375, FOI11_14345, FWK02_07210, GP944_10720, GP979_06075, GRW05_02535, HMV95_16245, J0541_003194, JNP96_10835 EC: 3.6.4
UniProt
Find proteins for A0A024L3Y3 (Escherichia coli) Explore A0A024L3Y3  Go to UniProtKB:  A0A024L3Y3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	B [auth G], C [auth H]	234	Escherichia coli	Mutation(s): 0  Gene Names: rpoA, FTV90_00720, FTV93_20930 EC: 2.7.7.6
UniProt
Find proteins for A0A5B9AW69 (Escherichia coli) Explore A0A5B9AW69  Go to UniProtKB:  A0A5B9AW69

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	D [auth I]	1,340	Escherichia coli	Mutation(s): 0  Gene Names: rpoB EC: 2.7.7.6
UniProt
Find proteins for C3SIA7 (Escherichia coli) Explore C3SIA7  Go to UniProtKB:  C3SIA7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	E [auth J]	1,358	Escherichia coli	Mutation(s): 0  Gene Names: rpoC EC: 2.7.7.6
UniProt
Find proteins for A0A369F490 (Escherichia coli) Explore A0A369F490  Go to UniProtKB:  A0A369F490

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	F [auth K]	91	Escherichia coli	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: 6
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')	G [auth R]	20	synthetic construct

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (49-MER)	H [auth N]	64	synthetic construct

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (55-MER)	I [auth T]	64	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	K [auth J], L [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	J	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Brewer, J.J., Darst, S.A., Campbell, E.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release