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- PDB-3jch: Cryo-EM structure of the magnesium channel CorA in the magnesium-... -

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Basic information

Entry
Database: PDB / ID: 3jch
TitleCryo-EM structure of the magnesium channel CorA in the magnesium-free, asymmetric open state II
ComponentsMagnesium transport protein CorA
KeywordsTRANSPORT PROTEIN / membrane protein / ion channel / magnesium channel / pentameric complex / symmetry vs. asymmetry / conformational change / gating mechanism / direct electron detector / K2
Function / homology
Function and homology information


magnesium ion transmembrane transport / cobalt ion transport / cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / cobalt ion binding / protein homooligomerization / magnesium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Magnesium/cobalt transport protein CorA / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.06 Å
AuthorsMatthies, D. / Perozo, E. / Subramaniam, S.
CitationJournal: Cell / Year: 2016
Title: Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating.
Authors: Doreen Matthies / Olivier Dalmas / Mario J Borgnia / Pawel K Dominik / Alan Merk / Prashant Rao / Bharat G Reddy / Shahidul Islam / Alberto Bartesaghi / Eduardo Perozo / Sriram Subramaniam /
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+)- ...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.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id / _em_software.name
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Magnesium transport protein CorA
B: Magnesium transport protein CorA
C: Magnesium transport protein CorA
D: Magnesium transport protein CorA
E: Magnesium transport protein CorA


Theoretical massNumber of molelcules
Total (without water)207,4905
Polymers207,4905
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Magnesium transport protein CorA


Mass: 41498.082 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: corA, TM_0561 / Plasmid: CorA-pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) PlysS / References: UniProt: Q9WZ31

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CorA from Thermotoga maritima in the absence of magnesium, state II
Type: COMPLEX / Details: One homopentamer of CorA / Synonym: CorA
Molecular weightValue: 0.2 MDa / Experimental value: NO
Buffer solutionName: 50 mM HEPES, pH 7.3, 150 mM NaCl, 1 mM EDTA, 0.5 mM DDM
pH: 7.3
Details: 50 mM HEPES, pH 7.3, 150 mM NaCl, 1 mM EDTA, 0.5 mM DDM
SpecimenConc.: 3.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 300 mesh Cu R1.2/1.3 holey carbon grids from Quantifoil, plasma-cleaned
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temp: 90 K / Humidity: 86 %
Details: Grids were blotted at 4 degrees Celsius for 7 seconds after a 10-second pre-blotting period, then plunge-frozen in liquid ethane.
Method: Grids were blotted at 4 degrees Celsius for 7 seconds after a 10-second pre-blotting period, then plunge-frozen in liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 15, 2014 / Details: Parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 5
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 890 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at 105,000 times magnification.
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen holder type: Liquid nitrogen-cooled / Temperature: 79.7 K / Temperature (max): 79.8 K / Temperature (min): 79.6 K
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Details: post-column Quantum GIF
EM imaging opticsEnergyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansNum. digital images: 2498

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2PHENIXmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
CTF correctionDetails: CTF parameters obtained from whole micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: RELION / Resolution: 7.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27416 / Nominal pixel size: 1.352 Å / Actual pixel size: 1.352 Å
Details: Final maps were calculated from two merged datasets. (Single particle details: The particles were selected using an automatic selection program. 3D classification, 3D refinement, and ...Details: Final maps were calculated from two merged datasets. (Single particle details: The particles were selected using an automatic selection program. 3D classification, 3D refinement, and postprocessing were done using RELION 1.3.) (Single particle--Applied symmetry: C1)
Symmetry type: POINT
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms6633 0 0 0 6633

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