5N78 | pdb_00005n78

Crystal structure of the cytosolic domain of the CorA Mg2+ channel from Escherichia coli in complex with magnesium and cobalt hexammine

• PDB DOI: https://doi.org/10.2210/pdb5N78/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2017-02-20 Released: 2017-07-12 
• Deposition Author(s): Lerche, M., Sandhu, H., Flockner, L., Hogbom, M., Rapp, M.
• Funding Organization(s): Swedish Research Council, Carl Tryggers stiftelse, Knut and Alice Wallenberg Foundation, Swedish Foundation for Strategic Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.218 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Structure and Cooperativity of the Cytosolic Domain of the CorA Mg(2+) Channel from Escherichia coli.

Lerche, M., Sandhu, H., Flockner, L., Hogbom, M., Rapp, M.

(2017) Structure 25: 1175-1186.e4

• PubMed: 28669631 
• DOI: https://doi.org/10.1016/j.str.2017.05.024
• Primary Citation Related Structures: 
  5N77, 5N78


• PubMed Abstract: 
  

  Structures of the Mg ²⁺ bound (closed) and apo (open) states of CorA suggests that channel gating is accomplished by rigid-body motions between symmetric and asymmetric assemblies of the cytosolic portions of the five subunits in response to ligand (Mg ²⁺ ) binding/unbinding at interfacial sites. Here, we structurally and biochemically characterize the isolated cytosolic domain from Escherichia coli CorA. The data reveal an Mg ²⁺ -ligand binding site located in a novel position between each of the five subunits and two Mg ²⁺ ions trapped inside the pore. Soaking experiments show that cobalt hexammine outcompetes Mg ²⁺ at the pore site closest to the membrane. This represents the first structural information of how an analog of hexa-hydrated Mg ²⁺ (and competitive inhibitor of CorA) associates to the CorA pore. Biochemical data on the isolated cytoplasmic domain and full-length protein suggests that gating of the CorA channel is governed cooperatively.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden.
Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content 

• Total Structure Weight: 152.11 kDa 
• Atom Count: 10,611 
• Modeled Residue Count: 1,282 
• Deposited Residue Count: 1,285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium transport protein CorA	A, B, C, D, E	257	Escherichia coli	Mutation(s): 0  Gene Names: corA, b3816, JW3789 Membrane Entity: Yes
UniProt
Find proteins for P0ABI4 (Escherichia coli (strain K12)) Explore P0ABI4  Go to UniProtKB:  P0ABI4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	AA [auth E], BA [auth E], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D], Z [auth E]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
PG0	L [auth B], Q [auth C], Y [auth E]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
MG	F [auth A], G [auth A], K [auth B], P [auth C], T [auth D], X [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.218 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.721	α = 90
b = 117.316	β = 103.14
c = 91.858	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Lerche, M., Sandhu, H., Flockner, L., Hogbom, M., Rapp, M.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--
Carl Tryggers stiftelse	Sweden	--
Knut and Alice Wallenberg Foundation	Sweden	--
Swedish Foundation for Strategic Research	Sweden	--

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations