9ZP4 | pdb_00009zp4

E. coli RNA polymerase elongation complex containing the unnatural dZ:PTP base pair in a trigger-loop-closed conformation

PDB DOI: https://doi.org/10.2210/pdb9ZP4/pdb
EM Map EMD-74516: EMDB EMDataResource

Classification: TRANSCRIPTION/DNA/RNA
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-16 Released: 2026-09-02
Deposition Author(s): Li, Q., Benner, S.A., Wang, D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.42 Å
Resolution: 2.42 Å
Resolution: 2.42 Å
Resolution: 2.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural Basis of Transcription of the Hachimoji Eight-Letter Alphabet by E. coli RNA Polymerase

Li, Q., Benner, S.A., Wang, D.

To be published.

Macromolecule Content

Total Structure Weight: 382.15 kDa
Atom Count: 26,654
Modeled Residue Count: 3,256
Deposited Residue Count: 3,350
Unique protein chains: 4
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B [auth G]	231	Escherichia coli	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7Z4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C [auth I]	1,342	Escherichia coli	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8V2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D [auth J]	1,430	Escherichia coli	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8T7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E [auth K]	74	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A800
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 5
Non-template strand DNA	F [auth N]	11	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
RNA	G [auth R]	9	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
Template strand DNA	H [auth T]	22	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C5A( Subject of Investigation/LOI) Query on A1C5A Download:Ideal Coordinates CCD File SDF format, chain M [auth J] MOL2 format, chain M [auth J] mmCIF format, chain M [auth J]	M [auth J]	(5S)-2-amino-8-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}imidazo[1,2-a][1,3,5]triazin-4(8H)-one C₁₀ H₁₆ N₅ O₁₄ P₃ IQZUXNWUNRGQBD-DBRKOABJSA-N		Interactions Focus chain M [auth J] Interactions & Density Focus chain M [auth J]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth J] SDF format, chain J MOL2 format, chain I [auth J] MOL2 format, chain J mmCIF format, chain I [auth J] mmCIF format, chain J	I [auth J], J	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth J] Focus chain J Interactions & Density Focus chain I [auth J] Focus chain J
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth J] SDF format, chain L [auth J] MOL2 format, chain K [auth J] MOL2 format, chain L [auth J] mmCIF format, chain K [auth J] mmCIF format, chain L [auth J]	K [auth J], L [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth J] Focus chain L [auth J] Interactions & Density Focus chain K [auth J] Focus chain L [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.42 Å
Resolution: 2.42 Å
Resolution: 2.42 Å
Resolution: 2.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Li, Q.

Benner, S.A.

Wang, D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102362
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM148476
National Science Foundation (NSF, United States)	United States	MCB-2419300
National Science Foundation (NSF, United States)	United States	MCB-1939086
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R24GM154186