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- EMDB-19073: human TRPM4 LMNG ligand CA -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19073
Titlehuman TRPM4 LMNG ligand CA
Map data
Sample
  • Complex: homotetramer
Keywordstrpm / inhibitor / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsEkundayo B / Prakash A / Christian G / Anne FH / Sabrina G / Mey B / Daniela R / Martin L / Jean SR / Henning S ...Ekundayo B / Prakash A / Christian G / Anne FH / Sabrina G / Mey B / Daniela R / Martin L / Jean SR / Henning S / Hugues A / Dongchun N
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_177195 Switzerland
Swiss National Science FoundationNCCR TransCure (185544) Switzerland
CitationJournal: To Be Published
Title: Identification of a Binding Site for Small Molecule Inhibitors Targeting Human
Authors: Ekundayo B / Prakash A / Christian G / Anne FH / Sabrina G / Mey B / Daniela R / Martin L / Jean SR / Henning S / Hugues A / Dongchun N
History
DepositionDec 8, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19073.png

Downloads & links

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Map

FileDownload / File: emd_19073.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 280 pix.
= 331.996 Å		1.19 Å/pix.
x 280 pix.
= 331.996 Å		1.19 Å/pix.
x 280 pix.
= 331.996 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1857 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.40682 - 1.884709
Average (Standard dev.)0.00027340467 (±0.04394081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 331.996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19073_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_19073_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 : homotetramer

EntireName: homotetramer
Components
  • Complex: homotetramer

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Supramolecule #1: homotetramer

SupramoleculeName: homotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 kDa/nm

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bqv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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