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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: Nat Commun / Year: 2026
Title: CryoWriter: a robotic solution for improved Cryo-EM grid preparation.
Authors: Chinmaya Kv / Babatunde Ekundayo / Marta Di Fabrizio / Inayathulla Mohammed / Julika Radecke / Henning Stahlberg / Massimo Kube /
Abstract: Cryo-electron microscopy (cryo-EM) structure determination relies on preparing thin, vitreous films of sample solution on EM grids. Cryo-EM is a mature technology, but preparing the grids remains a ...Cryo-electron microscopy (cryo-EM) structure determination relies on preparing thin, vitreous films of sample solution on EM grids. Cryo-EM is a mature technology, but preparing the grids remains a major bottleneck. Here, we evaluate the cryoWriter, a blotting-free, microfluidic grid-preparation robot that writes nanoliter volumes onto EM grids in a controlled environment. Using capillary-writing in spiral or line patterns, we prepared high-quality grids from minimal sample volumes and obtained near-atomic reconstructions for test specimens, including TMV, apoferritin, and the membrane protein TRPM4. We further demonstrate programmable deposition modes, such as writing the sample twice to boost particle density, or two-line writing for on-grid mixing to visualize time-resolved protein-ligand binding. In a challenging case (NrS-1 DNA polymerase), the cryoWriter grids exhibited reduced orientation bias relative to conventional blotting, enabling a more isotropic reconstruction. These results show that the cryoWriter provides a versatile platform for reproducible low volume cryo-EM grid preparation and for on-grid biochemical workflows.
History
DepositionSep 3, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 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

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8518 Å
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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
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Half map: #2

Fileemd_54984_half_map_1.map
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Half map: #1

Fileemd_54984_half_map_2.map
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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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