Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 25.64 kDa 
• Atom Count: 1337 
• Modelled Residue Count: 154 
• Deposited Residue Count: 218 
• Unique protein chains: 2

4X8K

Mycobacterium tuberculosis RbpA-SID in complex with SigmaA domain 2

• PDB DOI: 10.2210/pdb4X8K/pdb

• Classification: TRANSCRIPTION ACTIVATOR
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-10 Released: 2015-06-03 
• Deposition Author(s): Hubin, E.A., Flack, J.E., Tabib-Salazar, A., Paget, M.S., Darst, S.A., Campbell, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.231 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA.

Hubin, E.A., Tabib-Salazar, A., Humphrey, L.J., Flack, J.E., Olinares, P.D., Darst, S.A., Campbell, E.A., Paget, M.S.

(2015) Proc Natl Acad Sci U S A 112: 7171-7176

• PubMed: 26040003 
• DOI: 10.1073/pnas.1504942112
• Primary Citation of Related Structures:  
  4X8K


• PubMed Abstract: 
  

Gene expression is highly regulated at the step of transcription initiation, and transcription activators play a critical role in this process. RbpA, an actinobacterial transcription activator that is essential in Mycobacterium tuberculosis (Mtb), binds selectively to group 1 and certain group 2 σ-factors. To delineate the molecular mechanism of RbpA, we show that the Mtb RbpA σ-interacting domain (SID) and basic linker are sufficient for transcription activation. We also present the crystal structure of the Mtb RbpA-SID in complex with domain 2 of the housekeeping σ-factor, σ(A). The structure explains the basis of σ-selectivity by RbpA, showing that RbpA interacts with conserved regions of σ(A) as well as the nonconserved region (NCR), which is present only in housekeeping σ-factors. Thus, the structure is the first, to our knowledge, to show a protein interacting with the NCR of a σ-factor. We confirm the basis of selectivity and the observed interactions using mutagenesis and functional studies. In addition, the structure allows for a model of the RbpA-SID in the context of a transcription initiation complex. Unexpectedly, the structural modeling suggests that RbpA contacts the promoter DNA, and we present in vivo and in vitro studies supporting this finding. Our combined data lead to a better understanding of the mechanism of RbpA function as a transcription activator.

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Organizational Affiliation: 

School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor SigA	A	129	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: sigA, mysA, rpoD, rpoV, MT2777
UniProt
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGI1  Go to UniProtKB:  P9WGI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase-binding protein RbpA	B	89	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: rbpA, MT2110
UniProt
Find proteins for P9WHJ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHJ5  Go to UniProtKB:  P9WHJ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.231 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.459	α = 90
b = 84.459	β = 90
c = 73.701	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-10 
• Released Date: 2015-06-03 
Deposition Author(s): Hubin, E.A., Flack, J.E., Tabib-Salazar, A., Paget, M.S., Darst, S.A., Campbell, E.A.

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-06-17
  Changes: Database references
• Version 1.2: 2015-06-24
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description, Source and taxonomy