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- EMDB-6552: Cryo-EM structure of the magnesium channel CorA in the magnesium-... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6552 | |||||||||
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Title | Cryo-EM structure of the magnesium channel CorA in the magnesium-free asymmetric open state I | |||||||||
![]() | Reconstruction of Thermotoga maritima CorA in the absence of magnesium resulting in at least two conformations; here state I | |||||||||
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![]() | membrane protein / ion channel / magnesium channel / pentameric complex / symmetry vs. asymmetry / conformational change / direct electron detector / K2 / single-particle cryo-electron microscopy | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.06 Å | |||||||||
![]() | Matthies D / Dalmas O / Borgnia MJ / Dominik PK / Merk A / Rao P / Reddy BG / Islam S / Bartesaghi A / Perozo E / Subramaniam S | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.5 KB 12.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() ![]() | 167.2 KB 397.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jcgMC ![]() 6551C ![]() 6553C ![]() 3jcfC ![]() 3jchC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of Thermotoga maritima CorA in the absence of magnesium resulting in at least two conformations; here state I | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.352 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : CorA from Thermotoga maritima in the absence of magnesium, state I
Entire | Name: CorA from Thermotoga maritima in the absence of magnesium, state I |
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Components |
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-Supramolecule #1000: CorA from Thermotoga maritima in the absence of magnesium, state I
Supramolecule | Name: CorA from Thermotoga maritima in the absence of magnesium, state I type: sample / ID: 1000 / Details: Detergent-solubilized, purified protein / Oligomeric state: One homopentamer of CorA / Number unique components: 1 |
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Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: CorA
Macromolecule | Name: CorA / type: protein_or_peptide / ID: 1 / Name.synonym: Magnesium Channel CorA / Number of copies: 5 / Oligomeric state: Pentamer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 200 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Cobalt/magnesium transport protein CorA / InterPro: Magnesium/cobalt transport protein CorA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.7 mg/mL |
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Buffer | pH: 7.3 / Details: 50 mM HEPES, 150 mM NaCl, 1 mM EDTA, 0.5 mM DDM |
Grid | Details: 300 mesh Cu R1.2/1.3 holey carbon grids from Quantifoil, plasma-cleaned |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 86 % / Chamber temperature: 90 K / Instrument: LEICA EM GP 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
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 79.6 K / Max: 79.8 K / Average: 79.7 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 105,000 times magnification. Legacy - Electron beam tilt params: 5 |
Specialist optics | Energy filter - Name: Gatan, Inc. / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Details | Parallel beam illumination |
Date | Oct 15, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number real images: 2498 / Average electron dose: 40 e/Å2 Details: Every image is the average of 38 frames recorded by the direct electron detector. The total exposure time was 15.2 seconds, and intermediate frames were recorded every 0.4 seconds. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.89 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder: Liquid nitrogen-cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |