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- EMDB-18257: Cryo-EM structure of the magnesium channel CtMrs2 in the open state -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-18257
TitleCryo-EM structure of the magnesium channel CtMrs2 in the open state
Map data
Sample
  • Complex: Mrs2 homo-pentamer
    • Protein or peptide: Magnesium channel Mrs2
  • Ligand: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
  • Ligand: MAGNESIUM ION
KeywordsMagnesium channel Mrs2 / MEMBRANE PROTEIN
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsGourdon P / Li P
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionAug 18, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18257.png

Downloads & links

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Map

FileDownload / File: emd_18257.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342.64 Å		0.86 Å/pix.
x 400 pix.
= 342.64 Å		0.86 Å/pix.
x 400 pix.
= 342.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8566 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.8318644 - 1.487435
Average (Standard dev.)0.0005695765 (±0.026269365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18257_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18257_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mrs2 homo-pentamer

EntireName: Mrs2 homo-pentamer
Components
  • Complex: Mrs2 homo-pentamer
    • Protein or peptide: Magnesium channel Mrs2
  • Ligand: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mrs2 homo-pentamer

SupramoleculeName: Mrs2 homo-pentamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Macromolecule #1: Magnesium channel Mrs2

MacromoleculeName: Magnesium channel Mrs2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 49.090285 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: SGFSSEESSG RLTWRELLFG SGARKQSEAM KEEEIMMRLQ EDSGAIFQRR SLTSKAALDP RLRCTEVDGN GNVIMVDGEL KKSELIAKY GLLPRDLRKI DSSNLPHILV RPSAILINLL HLKVLIKHDR VLLFDVYGST SSYPQSAFMY DLQGKLQQKQ T GGANSLPY ...String:
SGFSSEESSG RLTWRELLFG SGARKQSEAM KEEEIMMRLQ EDSGAIFQRR SLTSKAALDP RLRCTEVDGN GNVIMVDGEL KKSELIAKY GLLPRDLRKI DSSNLPHILV RPSAILINLL HLKVLIKHDR VLLFDVYGST SSYPQSAFMY DLQGKLQQKQ T GGANSLPY EFRALEAVLM SVTAELEADF EAVRDPVIRI LSELEDDIDR EKLRILLVLS KRVSTFEQKA KLVRDAIEEL LE ADDDLAA MYLTEKTHDL YRGEDDHTEV ELLLESYHKL CDEVVQEASN LVSSIRNTEE IIRAILDANR NSLMLLDLKF SIG TLGLAM GTFLAGLYGM NLENFIEETN WGFGAITGLS TLLSLVVCWY GLAKLRKVQR VKMNGAGFTR HNHWFRDDST DVLL DPSNR ERLRKINMMK SHAKQKTAAA KKWPLNKL

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Macromolecule #2: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANO...

MacromoleculeName: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
type: ligand / ID: 2 / Number of copies: 5 / Formula: LOP
Molecular weightTheoretical: 661.89 Da
Chemical component information

ChemComp-LOP:
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / phospholipid*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.958 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116609
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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