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- EMDB-54984: Cryo-EM structure of the transient receptor potential melastatin ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54984
TitleCryo-EM structure of the transient receptor potential melastatin 4 (TRPM4) channel prepared using the cryoWriter automated grid preparation system with spiral-pattern writing
Map data
Sample
  • Complex: Transient receptor potential (TRP) melastatin 4 (TRPM4)
    • Protein or peptide: Transient receptor potential (TRP) melastatin 4 (TRPM4)
Keywordsautomated grid preparation / TRPM4 / cryo-EM / cryoWriter / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsChinmaya KV / Ekundayo B / Di Fabrizio M / Mohammed I / Radecke J / Stahlberg H / Kube M
Funding support Switzerland, European Union, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_200628 Switzerland
European Research Council (ERC)101118656European Union
CitationJournal: To Be Published
Title: CryoWriter: A Robotic Solution for Improved Cryo-EM Grid Preparation
Authors: Chinmaya KV / Ekundayo B / Di Fabrizio M / Mohammed I / Radecke J / Stahlberg H / Kube M
History
DepositionSep 3, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54984.png

Downloads & links

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Map

FileDownload / File: emd_54984.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 440 pix.
= 374.792 Å		0.85 Å/pix.
x 440 pix.
= 374.792 Å		0.85 Å/pix.
x 440 pix.
= 374.792 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8518 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.181
Minimum - Maximum-0.7395916 - 1.0621921
Average (Standard dev.)0.0019524283 (±0.01947225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 374.79202 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54984_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54984_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54984_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Transient receptor potential (TRP) melastatin 4 (TRPM4)

EntireName: Transient receptor potential (TRP) melastatin 4 (TRPM4)
Components
  • Complex: Transient receptor potential (TRP) melastatin 4 (TRPM4)
    • Protein or peptide: Transient receptor potential (TRP) melastatin 4 (TRPM4)

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Supramolecule #1: Transient receptor potential (TRP) melastatin 4 (TRPM4)

SupramoleculeName: Transient receptor potential (TRP) melastatin 4 (TRPM4)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 536 kDa/nm

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Macromolecule #1: Transient receptor potential (TRP) melastatin 4 (TRPM4)

MacromoleculeName: Transient receptor potential (TRP) melastatin 4 (TRPM4)
type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RSFHLEASLM DALLNDRPE F VRLLISHG LS LGHFLTP MRL AQLYSA APSN SLIRN LLDQA SHSA GTKAPA LKG GAAELRP PD VGHVLRML L GKMCAPRYP SGGAWDPHPG QGFGESMYL L SDKATSPL SL DAGLGQA PWS DLLLWA LLLN RAQMA ...String:
RSFHLEASLM DALLNDRPE F VRLLISHG LS LGHFLTP MRL AQLYSA APSN SLIRN LLDQA SHSA GTKAPA LKG GAAELRP PD VGHVLRML L GKMCAPRYP SGGAWDPHPG QGFGESMYL L SDKATSPL SL DAGLGQA PWS DLLLWA LLLN RAQMA MYFWE MGSN AVSSAL GAC LLLRVMA RL EPDAEEAA R RKDLAFKFE GMGVDLFGEC YRSSEVRAA R LLLRRCPL WG DATCLQL AMQ ADARAF FAQD GVQSL LTQKW WGDM ASTTPI WAL VLAFFCP PL IYTRLITF R KSEEEPTRE ELEFDMDSVI NGEGPVGTA D PAEKTPLG VP RQSGRPG CCG GRCGGR RCLR RWFHF WGAPV TIFM GNVVSY LLF LLLFSRV LL VDFQPAPP G SLELLLYFW AFTLLCEELR QGLSGGGGS L ASGGPGPG HA SLSQRLR LYL ADSWNQ CDLV ALTCF LLGVG CRLT PGLYHL GRT VLCIDFM VF TVRLLHIF T VNKQLGPKI VIVSKMMKDV FFFLFFLGV W LVAYGVAT EG LLRPRDS DFP SILRRV FYRP YLQIF GQIPQ EDMD VALMEH SNC SSEPGFW AH PPGAQAGT C VSQYANWLV VLLLVIFLLV ANILLVNLL I AMFSYTFG KV QGNSDLY WKA QRYRLI REFH SRPAL APPFI VISH LRLLLR QLC RRPRSPQ PS SPALEHFR V YLSKEAERK LLTWESVHKE NFLLARARD K RESDSERL KR TSQKVDL ALK QLGHIR EY

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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

Concentration6 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 0.5 µm / Nominal magnification: 165000
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

Particle selectionNumber selected: 695101
CTF correctionSoftware - Name: cryoSPARC (ver. v4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 69878
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

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