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- PDB-4cy4: The Cryo-Electron Microscopy Structure of the CorA channel from M... -

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Basic information

Entry
Database: PDB / ID: 4cy4
TitleThe Cryo-Electron Microscopy Structure of the CorA channel from Methanocaldococcus jannaschii at 21.6 Angstrom in low magnesium.
ComponentsMAGNESIUM TRANSPORT PROTEIN CORAMagnesium transporter
KeywordsMEMBRANE PROTEIN / MAGNESIUM ION CHANNEL
Function / homology
Function and homology information


cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / cobalt ion binding / magnesium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Magnesium/cobalt transport protein CorA / CorA, cytoplasmic domain / CorA, transmembrane region / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 21.6 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E
AuthorsCleverley, R.M. / Kean, J. / Shintre, C.A. / Baldock, C. / Derrick, J.P. / Ford, R.C. / Prince, S.M.
CitationJournal: Biochim Biophys Acta / Year: 2015
Title: The Cryo-EM structure of the CorA channel from Methanocaldococcus jannaschii in low magnesium conditions.
Authors: Robert M Cleverley / James Kean / Chitra A Shintre / Clair Baldock / Jeremy P Derrick / Robert C Ford / Stephen M Prince /
Abstract: CorA channels are responsible for the uptake of essential magnesium ions by bacteria. X-ray crystal structures have been resolved for two full-length CorA channels, each in a non-conducting state ...CorA channels are responsible for the uptake of essential magnesium ions by bacteria. X-ray crystal structures have been resolved for two full-length CorA channels, each in a non-conducting state with magnesium ions bound to the protein: These structures reveal a homo-pentameric quaternary structure with approximate 5-fold rotational symmetry about a central pore axis. We report the structure of the detergent solubilized Methanocaldococcus jannaschii CorA channel determined by Cryo-Electron Microscopy and Single Particle Averaging, supported by Small Angle X-ray Scattering and X-ray crystallography. This structure also shows a pentameric channel but with a highly asymmetric domain structure. The asymmetry of the domains includes differential separations between the trans-membrane segments, which reflects mechanical coupling of the cytoplasmic domain to the trans-membrane domain. This structure therefore reveals an important aspect of the gating mechanism of CorA channels by providing an indication of how the absence of magnesium ions leads to major structural changes.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2626
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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)185,9135
Polymers185,9135
Non-polymers00
Water0
1


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

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Components

#1: Protein
MAGNESIUM TRANSPORT PROTEIN CORA / Magnesium transporter / Coordinate model: Cα atoms only


Mass: 37182.586 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: RECOMBINANTLY OVER-EXPRESSED PROTEIN, SOLUBILIZED FROM MEMBRANE FRACTION. PURIFIED BY AFFINITY (HIS-TAG), SIZE EXCLUSION CHROMATOGRAPHY. PROTEOLYTIC TAG CLEAVEAGE.
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Description: PCR FROM GENOMIC DNA / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: Q58439

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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 CHANNEL FROM METHANOCALDOCOCCUS JANNASCHII / Type: COMPLEX
Buffer solutionName: 200MM NACL, 20MM TRIS/HCL, 0.04% DODECYLMALTOSIDE ( DDM)
pH: 8
Details: 200MM NACL, 20MM TRIS/HCL, 0.04% DODECYLMALTOSIDE ( DDM)
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jun 5, 2009 / Details: LOW DOSE MODE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4800 nm / Nominal defocus min: 3300 nm
Specimen holderTemperature: 100 K
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 28

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2EMAN3D reconstruction
CTF correctionDetails: WITH REFERENCE TO X-RAY SCATTERING CURVE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D RECONSTRUCTION FROM RANDOMLY ORIENTED PARTICLE IMAGES
Resolution: 21.6 Å / Num. of particles: 44064 / Nominal pixel size: 3.5 Å / Actual pixel size: 3.5 Å
Details: THE HIGH-RES MJCORA PDB 4EV6 STRUCTURE WAS DOCKED AS AN UNMODIFIED RIGID BODY. THERE ARE DIFFERENCES IN THE CRYO- EM AND CRYSTAL STRUCTURE DUE TO DIFFERENCES IN SOLUTION CONDITIONS ...Details: THE HIGH-RES MJCORA PDB 4EV6 STRUCTURE WAS DOCKED AS AN UNMODIFIED RIGID BODY. THERE ARE DIFFERENCES IN THE CRYO- EM AND CRYSTAL STRUCTURE DUE TO DIFFERENCES IN SOLUTION CONDITIONS SPECIFICALLY MG ION CONCENTRATION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2626. (DEPOSITION ID: 12440).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--DOCKING OF X-RAY CRYSTAL STRUCTURE
Atomic model buildingPDB-ID: 4EV6

4ev6

RefinementHighest resolution: 21.6 Å
Refinement stepCycle: LAST / Highest resolution: 21.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 0 0 1574

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