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- EMDB-2626: The Cryo-Electron Microscopy Structure of the CorA channel from M... -

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Basic information

Entry
Database: EMDB / ID: EMD-2626
TitleThe Cryo-Electron Microscopy Structure of the CorA channel from Methanocaldococcus jannaschii at 21.6 Angstrom in low magnesium.
Map dataSingle particle cryo-electron microscopy map of the CorA channel from Methanocaldococcus jannaschii
Sample
  • Sample: CorA channel from Methanocaldococcus jannaschii
  • Protein or peptide: Magnesium transport protein CorA
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 / 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 speciesMethanocaldococcus jannaschii (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 21.6 Å
AuthorsCleverley RM / Kean J / Shintre CA / Baldock C / Derrick JP / Ford RC / Prince SM
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 8, 2014-
Header (metadata) releaseApr 23, 2014-
Map releaseMay 6, 2015-
UpdateJul 22, 2015-
Current statusJul 22, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.125
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4cy4
  • Surface level: 0.125
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2626.jpg

Downloads & links

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Map

FileDownload / File: emd_2626.map.gz / Format: CCP4 / Size: 450.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle particle cryo-electron microscopy map of the CorA channel from Methanocaldococcus jannaschii
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
3.5 Å/pix.
x 49 pix.
= 171.5 Å		3.5 Å/pix.
x 49 pix.
= 171.5 Å		3.5 Å/pix.
x 49 pix.
= 171.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125 / Movie #1: 0.125
Minimum - Maximum-0.87796277 - 5.19715738
Average (Standard dev.)0.09105561 (±0.45542145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-24-24-24
Dimensions494949
Spacing494949
CellA=B=C: 171.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z494949
origin x/y/z0.0000.0000.000
length x/y/z171.500171.500171.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S312
start NC/NR/NS-24-24-24
NC/NR/NS494949
D min/max/mean-0.8785.1970.091

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Supplemental data

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Sample components

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Entire : CorA channel from Methanocaldococcus jannaschii

EntireName: CorA channel from Methanocaldococcus jannaschii
Components
  • Sample: CorA channel from Methanocaldococcus jannaschii
  • Protein or peptide: Magnesium transport protein CorA

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Supramolecule #1000: CorA channel from Methanocaldococcus jannaschii

SupramoleculeName: CorA channel from Methanocaldococcus jannaschii / type: sample / ID: 1000
Details: Single peak in DDM detergent in size exclusion, analysed by PFO-PAGE electrophoresis
Oligomeric state: Pentamer / Number unique components: 1
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Magnesium transport protein CorA

MacromoleculeName: Magnesium transport protein CorA / type: protein_or_peptide / ID: 1 / Name.synonym: MjCorA
Details: Recombinantly over-expressed protein, solubilized from membrane fraction. Purified by affinity (His-tag), size exclusion chromatography. Proteolytic tag cleaveage.
Number of copies: 5 / Oligomeric state: Pentamer / Recombinant expression: Yes
Source (natural)Organism: Methanocaldococcus jannaschii (archaea) / Strain: ATCC 43067 / Location in cell: Plasma membrane
Molecular weightTheoretical: 37 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: STAR / Recombinant plasmid: pOPINF
SequenceUniProtKB: Cobalt/magnesium transport protein CorA / InterPro: Magnesium/cobalt transport protein CorA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8 / Details: 20mM Tris/HCl,200mM NaCl,0.04% DodecylMaltoside
GridDetails: Quantifoil R 1.3/2 holey carbon-coated EM grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK I
Method: Blotted twice with Whatman No.1 filter paper for 1s each time

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMax: 104 K
DetailsLow dose mode
DateJun 5, 2009
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 28
Details: 4k by 4k pixel each pixel maps to 3.5 by 3.5 Angstroms
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.8 µm / Nominal defocus min: 3.3 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsModel based particle picking based an ab-initio model generated from a Small Angle Scattering
CTF correctionDetails: With reference to X-ray scattering curve
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.6 Å / Resolution method: OTHER / Software - Name: EMAN / Details: Initial model derived from SAXS envelope / Number images used: 44064
Final two d classificationNumber classes: 490
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4ev6


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E
SoftwareName: UCSF Chimera
DetailsThe coordinates of the MjCorA pentamer from PDB entry 4ev6 were positioned manually within the envelope. The fit was adjusted automatically by maximizing the correlation of the EM map with a map calculated from 4ev6 at a resolution of 21.6 Angstroms.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Target criteria: Maximum correlation of map calculated from coordinates
Output model

PDB-4cy4:
The Cryo-Electron Microscopy Structure of the CorA channel from Methanocaldococcus jannaschii at 21.6 Angstrom in low magnesium.

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