Skip to main content

 3JCF | pdb_00003jcf

Cryo-EM structure of the magnesium channel CorA in the closed symmetric magnesium-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3JCF

This is version 1.3 of the entry. See complete history. 

Literature

Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating.

Matthies, D., Dalmas, O., Borgnia, M.J., Dominik, P.K., Merk, A., Rao, P., Reddy, B.G., Islam, S., Bartesaghi, A., Perozo, E., Subramaniam, S.

(2016) Cell 164: 747-756

  • DOI: https://doi.org/10.1016/j.cell.2015.12.055
  • Primary Citation Related Structures: 
    3JCF, 3JCG, 3JCH

  • PubMed Abstract: 

    CorA, the major Mg(2+) uptake system in prokaryotes, is gated by intracellular Mg(2+) (KD ∼ 1-2 mM). X-ray crystallographic studies of CorA show similar conformations under Mg(2+)-bound and Mg(2+)-free conditions, but EPR spectroscopic studies reveal large Mg(2+)-driven quaternary conformational changes. Here, we determined cryo-EM structures of CorA in the Mg(2+)-bound closed conformation and in two open Mg(2+)-free states at resolutions of 3.8, 7.1, and 7.1 Å, respectively. In the absence of bound Mg(2+), four of the five subunits are displaced to variable extents (∼ 10-25 Å) by hinge-like motions as large as ∼ 35° at the stalk helix. The transition between a single 5-fold symmetric closed state and an ensemble of low Mg(2+), open, asymmetric conformational states is, thus, the key structural signature of CorA gating. This mechanism is likely to apply to other structurally similar divalent ion channels.


  • Organizational Affiliation: 
    • Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 207.81 kDa 
  • Atom Count: 14,228 
  • Modeled Residue Count: 1,745 
  • Deposited Residue Count: 1,755 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Magnesium transport protein CorA
A, B, C, D, E
351Thermotoga maritimaMutation(s): 0 
Gene Names: corA, TM_0561
Membrane Entity: Yes 
UniProt
Find proteins for Q9WZ31 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZ31 
Go to UniProtKB:  Q9WZ31
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZ31
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth B]
I [auth B]
J [auth C]
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth C],
K [auth C],
L [auth D],
M [auth D],
N [auth E],
O [auth E],
P [auth E],
Q [auth E],
R [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description