5CIZ | pdb_00005ciz

E. coli RNA polymerase alpha subunit CTD in complex with CAP and DNA: A(5)-tract binding site for alpha CTD

• PDB DOI: https://doi.org/10.2210/pdb5CIZ/pdb
• NAKB: 5CIZ

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


• Deposited: 2015-07-13 Released: 2016-06-29 
• Deposition Author(s): Napoli, A.A., Lawson, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.01 Å
• R-Value Free: 
  0.214 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element

Lara-Gonzalez, S., Machado, A.C.D., Rao, S., Napoli, A.A., Birktoft, J., Di Felice, R., Rohs, R., Lawson, C.L.

(2020) Biochemistry 

• DOI: https://doi.org/10.1021/acs.biochem.0c00571

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 46.74 kDa 
• Atom Count: 3,099 
• Modeled Residue Count: 321 
• Deposited Residue Count: 337 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-activated global transcriptional regulator CRP	A	209	Escherichia coli K-12	Mutation(s): 0  Gene Names: crp, cap, csm, b3357, JW5702
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12)) Explore P0ACJ8  Go to UniProtKB:  P0ACJ8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	B	84	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: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*TP*TP*TP*TP*GP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')	C [auth D]	20	Escherichia coli

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*CP*AP*AP*AP*AP*AP*G)-3')	D [auth E]	24	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	E [auth A]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.01 Å
• R-Value Free:  0.214 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.312	α = 90
b = 176.312	β = 90
c = 158.493	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Napoli, A.A., Lawson, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM21589

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2020-11-25
  Changes: Database references
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description