Biological Assembly 1  

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

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 64.34 kDa 
• Atom Count: 3709 
• Modelled Residue Count: 466 
• Deposited Residue Count: 562 
• Unique protein chains: 1

5C3C

Structural characterization of a newly identified component of alpha-carboxysomes: The AAA+ domain Protein cso-CbbQ

• PDB DOI: 10.2210/pdb5C3C/pdb

• Classification: PROTEIN BINDING
• Organism(s): Halothiobacillus neapolitanus c2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-17 Released: 2015-11-18 
• Deposition Author(s): Sutter, M., Kerfeld, C.A.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.283 
• R-Value Work: 0.226 
• R-Value Observed: 0.231 

Literature

Structural Characterization of a Newly Identified Component of alpha-Carboxysomes: The AAA+ Domain Protein CsoCbbQ.

Sutter, M., Roberts, E.W., Gonzalez, R.C., Bates, C., Dawoud, S., Landry, K., Cannon, G.C., Heinhorst, S., Kerfeld, C.A.

(2015) Sci Rep 5: 16243-16243

• PubMed: 26538283 
• DOI: 10.1038/srep16243
• Primary Citation of Related Structures:  
  5C3C


• PubMed Abstract: 
  

Carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and its substrate CO2 within a proteinaceous shell. They are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. Carboxysomes consist of a protein shell that encapsulates several hundred molecules of RuBisCO, and contain carbonic anhydrase and other accessory proteins. Genes coding for carboxysome shell components and the encapsulated proteins are typically found together in an operon. The α-carboxysome operon is embedded in a cluster of additional, conserved genes that are presumably related to its function. In many chemoautotrophs, products of the expanded carboxysome locus include CbbO and CbbQ, a member of the AAA+ domain superfamily. We bioinformatically identified subtypes of CbbQ proteins and show that their genes frequently co-occur with both Form IA and Form II RuBisCO. The α-carboxysome-associated ortholog, CsoCbbQ, from Halothiobacillus neapolitanus forms a hexamer in solution and hydrolyzes ATP. The crystal structure shows that CsoCbbQ is a hexamer of the typical AAA+ domain; the additional C-terminal domain, diagnostic of the CbbQ subfamily, structurally fills the inter-monomer gaps, resulting in a distinctly hexagonal shape. We show that CsoCbbQ interacts with CsoCbbO and is a component of the carboxysome shell, the first example of ATPase activity associated with a bacterial microcompartment.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CbbQ/NirQ/NorQ domain protein	A, B	281	Halothiobacillus neapolitanus c2	Mutation(s): 0  Gene Names: Hneap_0905
UniProt
Find proteins for D0KZ75 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2)) Explore D0KZ75  Go to UniProtKB:  D0KZ75

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.283 
• R-Value Work: 0.226 
• R-Value Observed: 0.231 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.913	α = 90
b = 171.913	β = 90
c = 53.565	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-17 
• Released Date: 2015-11-18 
Deposition Author(s): Sutter, M., Kerfeld, C.A.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-FG02-91ER20021

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence